I'll try to answer all the questions.
The blurriness is probably only in Chrome. I tried everything to disable it, but I can't get rid of it without upscaling the canvas. It looks sharp in Firefox.
Transitions between generated tilsets. Yes, it's kinda possible, but there is no user interface for it yet. It would be possible to interpolate between two tilesets, but it may look rather strange if the sprites are changing. For what particular use case do you think it would be useful?
The program accepts palettes up to 50 colors because that's the number of colors I could fit into 5 light levels with 256 values. Anything between 2 and 50 should work fine.
I have added a few more door templates, so if you keep randomizing a bit you should find a few doors.
The ship generator is too specific an art-style. It would only work if that's the exact style of ship you're going for.