EoSD - Compare the beggining of Eastern Dream to the part of Septette thats starts at 1:23 - it's very similar but slower.
PCB - I thought Sakura Sakura and Japanize dream were the same song "Sakura Sakura ~ Japanize Dream" Anyway, in "Sakura Sakura ~ Japanize Dream", at :30 you can hear a piano-ish melody in the background. This sounds very similar to "Bloom Nobly, Cherry Blossoms of Sumizome ~ Border of Life" at 1:05.
IN - This one I'm unsure about. Basically the piano in the beggining of Eternal Dream ~ Mystic Maple is "kind of" like the fast intro part of Lunatic Princess. But not really. I would note, however, that there are two final bosses, and that Mokou's theme has some similarity to Kaguya's. (They start kind of softly, then shift into a fast repetative intro) Otherwise idk, IN is just wierd.
PoFV - The intros to Another Dream and Eiki's theme are vaguely similar. Another Dream has a three note repetition at :29. Eiki's theme does the same thing at :50.
MoF - You agreed to that one earlier.
SA - Compare Future Dream at :22 to Nuclear Fusion at :50. Otherwise its more in the "feel" rather than direct similarity.
UFO - You agreed with that one too.
TD - No idea, unfamiliar with the soundtrack.
Clearly, some of these are just vaguely similar, but still the similarities are close enough (imo, anyway) Also I'm not familiar with Fairy Wars, if that even counts.
Sorry about the late reply I've had no internet access.
I can sort of get where you're coming from, and yes I agree with you noting the thematic similarity, which seems to be a trend for ZUN especially in the post-MoF games. However, there aren't really explicit links between the Stage 6 boss' themes and the
Staff Roll/Credits themes. (Nitpicking, but the
Ending themes are a different thing altogether.)
Some of the melodies and note progression do sound similar, but they are not the same thing. If anything, this looks like a case of seeing patterns that aren't there (there's a word for it too: Apophenia. Who knew?)
In fact, I had a similar experience some time ago trying to find the "Touhou Theme" (the note progression in every single Menu Theme since EoSD (minus Hisoutensoku?) ) in the Stage 6 boss themes. This happened after I noticed how obvious these notes were in the main melodies of Miko and Mamizou's themes, as well as in Kaguya and Eirin's. needless to say there weren't any results elsewhere.
A few other things to point out:
IN -
Mystic Maple is in fact based on PoDD's ending theme,
Maple Dream. Imagine my surprise when I cleared PoDD the first time.
GFW - Has no Staff Roll theme, but the Ending theme is a slower verion of the Menu theme.
......
GFW - Has no Staff Roll theme
Possibly-crazy stuff that you still haven't noticed until now
Just realised that GFW has no Staff Roll at all

. I've cleared it a number of times already and yet I've never actually noticed it.