You can generally play for hundreds of years, easily, especially if your NPR generation chance is low, something like 5%, and you have, at the very least, Star Swarm and Invaders off.  Precursors aren't that big of a problem in my experience.  I've done this myself, with one particular game that lasted about 250 years a few versions ago. 

The target also needs a mass driver, so you'll need to be able to transport a mass driver to the planet in question, which implies that you could just as easily invade with ground troops or bombard it from orbit.

You can only target your own colonies with mass drivers, so they can't even be used offensively

You can boost the accessability of the minerals on their worlds can you not? Though they themselves would need to exploit that. Could also terraform a few worlds for them nearby. High tech wrecks is also another option, but requires you to kill either your own ships or anothers ships nearby (which because theyd be watching, would probably plummet their diplomatic opinion of you)

I would just say that you're unlucky. It's possible to discover dozens of habitable worlds without encountering an NPR. It's possible for those NPRs to be small and utterly insignificant. But it's also possible to meet an NPR right next door to Sol and it's strong enough to whoop your ass.

Unfortunately, as far as I know, there's nothing you can do to boost an NPR, as you cannot give them new techs or industry through SM.

Playing 6.4x, you CAN still come across low tech procedurally spawned empires. I thought my fleet was bad, but then i end up getting caught in conflict with an AI... who sends only one ship is a single missile craft that slings 6 missile salvos at under 5000 km/s. Did i mention it's only active sensors were too big to see my fast attack craft?
And here i thought including fast attack craft in my military sortie would have not much use beyond a last resort.

My games usually have 20 to 25 systems, 1 high difficulty NPR. The last war lasted 18 months, ended in the total destruction of their homeworld.

1. My longest game is 111 years old. 111 discovered (by me) systems, 3 civilizations annexed (one was saved by that because their homeworld was glassed by Invaders), etc., etc. I dropped it because of two reasons: new version, and "someone spotted by someone, let's stop the clock". 10 NPRs, three types of spoilers and me don't go very well.

2. I usually negotiate for friendly status (before invading), the NPR surveys every system they can reach. Cue slowdown, and new NPRs (more slowdown), ruins (more interrupts), star swarms (even more interrupts)...
As for hostilities, they are usually... doing nothing, but sometimes they trigger interrupt.

3. NPR is always viable unless someone glasses their worlds and destroys their ships.

I've heard about people who have done 170-yr runs. I think it's possible to go even further, if you manage to manage NPRs.

About my experience:

#1 is actually one of the least disturbing of the problems: my empire grows larger, I need more time to maintain it, my computer needs more time to run it. It's fair.

#2 is the most annoying, especially the "00:01:00 potential something interrupt" when one ship tries to catch another ship but isn't able to (and I'll just say it's not epic at all). It's terrible experience.

#3 As of current game, errors don't bother me much. That's weird because they were ruining my games sometimes in previous versions.

#4: let me just copy the logs:

14th May 2057 14:29:01,Abadan,Abadan,Mineral Shortage (Tritanium) in Production of Mougo Anti-missile Missile at Abadan Prime
14th May 2057 14:29:01,Yousif,Yousif,Mineral Shortage (Gallicite) in Production of Bandersnatch Anti-missile Missile at Yousif Prime
14th May 2057 14:29:01,Yousif,Yousif,Mineral Shortage (Duranium) in Production of Convert Mine to Automated at Yousif Prime
14th May 2057 14:29:01,PortLouis,Unknown,Racial Wealth is negative. Production will be reduced accordingly until the debt is repaid.
14th May 2057 14:29:01,Sekhemkare,Unknown,Racial Wealth is negative. Production will be reduced accordingly until the debt is repaid.
14th May 2057 14:29:01,Grand Base,Unknown,Racial Wealth is negative. Production will be reduced accordingly until the debt is repaid.

When I captured Aargonar homeworld, I noticed one thing, called planetary missile stockpile. Who in their right mind can build 550000 AMMs?

#5: while they steal get everything they can from me:

14th May 2057 14:29:01,ZemSoy,Chi(1) Orionis,25 inactive Research Labs on Equation
14th May 2057 14:29:01,ZemSoy,S.W. Burnham 543,A team on S.W. Burnham 543-A III led by Louis Stokes has completed research into Microwave Focusing Technology 5
14th May 2057 14:29:01,Aargonar,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by HIP 21932 Aliens #207 <= hey, it's me!
14th May 2057 14:29:01,Abadan,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by Abadan Aliens #202
14th May 2057 14:29:01,Yousif,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by Yousif Aliens #202
14th May 2057 14:29:01,PortLouis,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Gliese 176 Aliens #214
14th May 2057 14:29:01,Aargonar,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Sol Aliens #222
14th May 2057 14:29:01,Abadan,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Abadan Aliens #202
14th May 2057 14:29:01,Yousif,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Yousif Aliens #202
14th May 2057 14:29:01,Vorkuta,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Vorkuta Aliens #214
14th May 2057 14:29:01,Muscida,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Muscida Aliens #202
14th May 2057 14:29:01,Vorkuta,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by Vorkuta Aliens #214
14th May 2057 14:29:01,Canal,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Canal Aliens #214
14th May 2057 14:29:01,Muscida,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by Muscida Aliens #202
14th May 2057 14:29:01,PortLouis,Unknown,Information on Microwave Focusing Technology 5 has been provided to us by PortLouis Aliens #215
14th May 2057 14:29:01,Sekhemkare,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Sekhemkare Aliens #222
14th May 2057 14:29:01,Grand Base,Unknown,Information on Microwave Focusing Technology 3 has been provided to us by Grand Base Aliens #222

they don't appear to develop\use new ship designs. Aargonar, for example, was still using Ion-powered ships, when I was flying around with Gas Core AM Engines.
Invasion becomes boring and NPRs look helpless after that.

#6 affects me the least: I'm starting to read huge logs and spend most of the time giving orders instead of advancing time. Doesn't make game any worse because I like to give orders. 

^{I could try a conventional longrun just to see how far can I get.}