Thanks for testing on hardware, DK. That's useful to know. I can try with a different ARM core and see if weird LSA/LEA values are also written.
Update: MAME's ARM core writes identical wacky LSA/LEA values. I changed my AICA so that on keyon if LSA > LEA it sets LEA to 0xffff and that seems to work for the Guilty Gear X tracks even if it's not what actually happens
Update 2: I hacked up the AEG monitor as Deunan recommended (scaling the result to 0-959) and both Takoron and the VF3 test rip seem to play properly now.