Yes, Alchemite will pass through you once you reach 9000 maximum.
Some levels of the Classic set have wormholes at player-level (like the original PowBall DeluXe). I've changed how this works recently and something might have broken. I'll test it now and it should be fixed in 2.04 if there's a problem. Some levels will trap you at the top once you go through one-way wormholes - this seems a bit crazy was intentional. You should drift back to to the bottom for the sub-game once the level is cleared.
Thanks for letting me know and don't hesitate to suggest anything else.