Looks like this will no longer be an issue in version 1.14.0 / 2.0 : http://aurora2.pentarch.org/index.php?topic=12523.msg154574#msg154574

Currently, newly generated races ignore the research speed modifier for their starting tech points and apply it only for subsequent research. For v2.0, the research modifier will be applied to starting tech points for NPRs, Star Swarm, Rakhas and Aether Raiders

Regardless of modifier, the minimum starting points are 100k for Rakhas, 120k for NPRs, 400k for Raiders and 600k for Swarm (to ensure that key components and the essential nature of the threat are preserved). Precursors start with 600k tech points or 20% greater than the maximum player race starting points, whichever is higher. Invaders start with 1m tech points or 50% greater than the maximum player race starting points, whichever is higher.

This change won't make much difference to the early game (or to Precursors/Invaders for most games), but it will mean that later-game NPRs and Swarm in particular are not overpowered in low research rate games. If the early game is a concern, the options for minimum player systems can be used.

If I recall, NPR tech levels are affected by game length. The research speed modifier affects only the player.

This isn't entirely true, as there are two different research speed modifiers: there is the global modifier set in the New Game Settings, which should affect all races, and then there is a race-specific modifier which affects only the (usually player) race. NPRs once created do generate research points based on the global modifier as well as e.g. the number of labs they have built.

Newly-generated NPRs however gain starting RP based on population and time since game start, and since the documentation on this is...scattered, shall we say, I'm not sure if this process is affected by the global modifier. If not, that would explain why a newly-generated Swarm race thoroughly outtechs a NPR which has existed since game start, since each new Swarm generates with its own technology level if I understand Swarm mechanics correctly.

Okay, I made a post about it some time ago and found it intriguing and challenging that newly generated species are so far ahead. But now the same thing happened with the swarm attacking a starting NPR. The starting NPR had ion drive ships with 15 cm lasers and no electronic warfare equipment, while the swarm was using solid core antimatter ships with 50 cm lasers and ewar 5.
That poor species got annihilated without ever hitting a ship with their lasers or ASMs. They had several million tons of military hardware around their homeworld, which was to absolutely no effect whatsoever. My fleet was at least able to fire their guns at a jump camp before being eaten alive.
To be frank: the starting tech level of these species must be affected by the game rules and the research speed set by the player. Otherways, you have to expect to see some (un)intended situations.

PS: Unique clowns are only funny once