Nice job! I recently got 2.6 billion up to Yashin's first form but I want to have a few more goes at getting the clear with Nur. Nice to have more competition.
As for scoring, thanks for bringing up a few points. On Normal the last phase is the only that triggers a coin drop based on multiplier, as you noted. I don't know if this is different on Hard mode, which adds an extra phase/life-bar for bosses and midbosses (aka the cube crew) - I say that because despite having a new 'final' phase, the original final (now the 3rd out of 4, if that makes sense) has the most destructible bullets, which means more chances for x16 milking. I haven't played Hard mode enough to see which is more lucrative.
I am not sure if you are actually getting 8x8 the amount of coins; I'd have to watch some replays in order to really see what's going on.
Boss phases nonetheless can still end with a multiplier, so it's good to get as many x8 bonuses as you can, especially once you get the coins to their max 10,000pt value.
As you noted, proximity to enemies can substitute for bullets. With Nur's familiars, this is how I can maintain a lot of x8 bonuses by get close to enemies and quickly tapping my familiar button and getting some hits in.
Every stage as 3 fairies. One before the midboss, one after, and one in the boss arena itself. Some are more hidden than others. Stage 1's second fairy is right after the midboss, hidden above the tree to your left (by one of the destructible graves). Fairy locations are marked by a faint shimmering or sparkling on the ground. This is not always easy to see (like in Lale's dark arena!).
As for Sonay revealing fairies, my guess is that those two instances enemies are overlapping the fairy location (the large yeti in st2, and the phantoms in st5) and as her familiar is attacking those enemies its attack overlaps the fairy reveal spot.
Finally, as for score, while I am not sure how 4billion is achieved yet, I can easily see 3billion being an optimal score with as few deaths as possible (dying and resetting the coin value can really put a dent in your score). I end the first stage with 500 million, and on average get about 500m per stage. If I can make it with fewer deaths and a clear, a 3 billion clear doesn't seem out of the ordinary. Otherwise you want to prolong the boss phases with destructible bullets as long as possible (on Normal e.g. Sonay's final phase, Selma's final, maybe Lale's second phase with the ghost spam).