When I leave a diplomatic ship in a home system it tends to get blown up before full communication is established. With contact in other systems I have got to the point of being considered freindly by at least one alien , it tends to help if they are several jumps away to cut down conflict over vital systems
I think a big factor is how your 'diplomatic ship' gets reported as a sensor contact.
For a example a 15,000 ton ship with military graded sensors, military engines, military J-Engine, cloak and a diplomacy module will be picked up by NPRs as being effectively the same as having a offensive capable military ship parked in their home system, as pretty much all components on that thing are screaming "Military ship" on sensors.
In one of my recent campaigns I fielded a joint stealth surveillance and diplomacy ship design that had ELINT, reduced thermal output military engines, long range EM sensor, cloak and a diplomacy module. As soon as a NPR detected the ship monitoring them on their sensors, they'd immediately react telling me the ship needs to leave immediately or be destroyed. Until they detected the ship, even though it was communicating with them and building diplomacy they had no problems.
I then fielded a 2nd design, this time with just reduced thermal output civilian engine and diplomacy module and sent it out. And they never said a thing about the ship being there even though I highly suspect the lack of cloak has meant they'd picked it up sitting there easily enough.
As far as the OP question of 'Is diplomacy fixed now?'..... it's a bit mixed. For example I've had situations where I have had colonies in systems neighbouring my empires home system with a few million population on them. My survey ships exploring generate a new NPR 3 or 4 systems away and within a year or two that new NPR has gated a path right up to my border colonies. Even with communications established and despite being flagged as a "Request/Demand leave" the NPRs will refuse to recognise things like a system with 2 planets with 300 automated mines with each sending their minerals to a populated planet with a population of 5-6 million as being 'evidence' that I have any actual activity in the system and will ignore my warning and begin setting up operations in the system themselves and then quickly deciding I am the one intruding.
Other times once I've had border colonies that have 100 million+ population and spawned a NPR that's quickly gated across 4-5 systems and made its way to my colony in a year or less since being spawned by my exploration ships, and the NPRs have happily listened to demands of leaving and respected my territory.
So diplomacy sort of works... but the NPRs criteria for what counts as evidence of another empire having operations in a system seems a bit off and really discourages on-going exploration whilst you got border colonies getting established as NPRs even friendly ones will just locust swarm over there in no time flat after being spawned via exploration and refuse to recognise millions of people and multiple mining operations as being note worthy.
