There should be some way to submit Wind Fortress (or boss attack) speedruns in the Sub-Games as these literally have TIMERS BUILT IN and lots of room for speedrunning. This is my opinion only so take it with a grain of salt.

https://www.speedrun.com/cave_story_time_attack_challenges problem solved

The time attack challenge board is already linked in the Sub-games page, although for some reason you have to check "Show unofficial releases" to see it.