No, the spawn point is fine. I've just played through the whole thing.
May I make a suggestion? It'd be better if you remove the left warp line in "Remember Super Gravitron?" - it's possible to do it without using that line, and I did it the hard way the first time.
EDIT: This isn't a problem with your level, but it's a problem with VVVVVV. Finishing with 21 trinkets only gets you one star for completion. You have to finish with exactly 20 to get two stars. Shame really, but you have to complete it at least once with 20 to get that second star. I don't think there's a way to fix it unless you can set Trinkets to 20 at the exact point you collect the final crew member?
Yeah, that's a shame, I found that out when it was kind of too late...
Anyway, I *know* it's possible to that room the hard way, but I wanted to hint at another solution. I'll think about it

I've done everything I wanted before releasing 1.0 now. I'll playtest tomorrow and in case I don't find any bugs, I'll release it!
Fixes since beta 2.0c:
* DIY VI Repair works. For sure this time! Really! I hope so...
* Saving in gravitrons works
* There's now a disclaimer in the ship about gravitron chaining
* There isn't random terminals missing in the ship anymore
* There's a little monologue right before ending the level to "justify" rescuing Victoria
* You cannot get the wrong music playing without editing the save file manually now. Eheheh... (Also, this "bug" exists in the main game in some places :3)
* Proper credits info
* The ship map coordinates is hidden until the ending now. Also hides the teleporter hub before you go there by yourself
* Made a very minor nerf to Spike Pit
* There isn't any obvious internal script trigger in the polar dimension entry anymore
* Fixed possibility to die in the secret area due to Inversed Floors being right above it (this wasn't supposed to be possible)
* Ship jukebox semi-works. I've yet to find out exactly how to light terminals manually, but you should at least be able to trigger them more than once now.
* Fixed VVVVVV 2.0 bug related to music stopping (mostly seen in time trial in the original game) affecting two of my internal scripts.
* Fixed a less brutal respawn if you manage to die after doing the first part of the dimension story without hitting a checkpoint.
* The locator now acknowledges the lack of a map in VVVVVV 2.0. I can't really do more than saying that 2.1 is recommended there, though...