I ended up stuck at the south-east energy fountain my first time because I ran out of missiles fighting the metroids (coming in with 230). Sometimes the drops are just really unlucky, but also I wasn't expecting so many metroids, especially being directly in my way and having to be destroyed! My subsequent attempt was fine though, I found that once I started being careful they did replenish faster than I was being worn down.
Incidentally I find it curious that the fountains refill energy but not missiles. Why alleviate energy grind, but not missile grind? It would also probably make this metroid drop RNG mostly not a problem, since there are a few fountains on that path.
I just finished a playthrough of version 1.0, notes here:
As far as the "secret" stuff:
Anyhow, really cool. I enjoyed it a lot. Thanks for all the hard work!