There might be a caveat to this caveat. I don't have AL, but I do run Double Deluxe Store Edition with MGS (Uni, OFB, various SPs) and the hacks seem to be fine. And my game appears to be stable.
Depends on the hacks used. Some of them are now ticking timebombs waiting to explode, though, as code will think it is running pre-AL, and therefore, fail spectacularly in certain cases.
I'm thinking there must be two (or more) versions of the store edition. The reason I ask is because I tried to use the DD no-CD cracks and they wouldn't work. Further investigations make it seem as though it is a post AL/MGS engine seeing as I had all the cheats and my user interface has things like the FT aspiration meter and grayed out spots for where things would go if I had those EPs. I also have use of BV jewelry (in CAS) and ceilings.
This is a different engine, no? Will very bad things™ happen using the hacks with a post AL/MSG engine?