Hmm, looks like Koishi's shot has an advantage in stage 5, where I had to bomb repeatedly as Reimu to clear the enemies. I'll probably try Koishi after finishing a Reimu run.
I'm not sure I see the border advantage with Koishi you mention, though-- at the start of stage 6, you had a slightly lower PIV (460k compared to 467k) and the same number of borders (the PIV is being multiplied by 4.1, indicating 31 successful borders) as in my failed clear. The 200m you gained seems to be mainly from stage 5 items and clearing. I wonder how many extra borders it'd be worth to spend those remaining lives on bullet cancels somewhere earlier?
There are no bonuses at the end of the game, not for lives remaining or anything. The score you see after beating the final boss is your final score.
How is this not a clear bonus? Screenshot from your replay. Assuming 60m of the 98,153,000 is the stage 6 bonus, that leaves 38,153,000 unaccounted for.
Edit:
Checking a few Lunatic videos posted earlier, the bonus was:
86,523,000 in FleetingGaze's Lunatic 1cc (finished 0/0, 352,110 PIV, 13,500 graze)
171,347,000 in Zigzagwolf's Lunatic 1cc (finished 4/1, 380,760 PIV, 16,039 graze)
236,207,000 in Jaimers' run with all last spells (finished 6/5, 362,530 PIV, 13,502 graze)
260,008,000 in Pruns' no-death Lunatic run (finished 8/3, 338,090 PIV, 10,059 graze)
These bonuses are rather irregular. Too irregular to be only based only on remaining resources. And yet they do approximately scale with resources (note that Pruns' 8/3 clear bonus is about 90m higher than Zigzagwolf's 4/1 clear bonus, which in turn is about 90m higher than FleetingGaze's 0/0 clear bonus).
I don't think 4 data points are enough to figure out a formula, though-- too many potentially relevant variables (including hidden values like the total number of borders).
Edit 2:
3,344,994,040 (still Reimu), with another silly game over. No major mistakes up to stage 6, and I reached Tensei with 1/0, which should've been plenty. Except I died to the first nonspell then again to the last frame of the survival,
as I captured it (the game did add the 37m spell bonus).