I think they're pretty much hardwired to do so.
For dumping cartridges I usually put a piece of tape on one of the cartridge lines so it doesn't autoboot, but I've found at least one cartridge that even with that autoboots.
It may be that being mapped on top of the basic rom it has some code there that takes on and boots the cartridge.
Not that I'm talking about dumping......
In the real hardware there are two ways for a cartridge to auto-start :
1) a lot of the cartridges (mostly games) are wired with the Q clock connected to the FIRQ line to cause them to auto start.
2) If the cartridge contains the characters 'DK' as the first two it is assumed to be a disk controler, and the firmware willinitialize it by jumping to $C002
However there are a third class of cartridge such as the "Alldream" assembler for the Dragon which **DO NOT** use either of these methods and are accessed from basic as needed just by EXECing their entry address. Currently it is impossible to use these in MESS as it assumes all cartridges will auto start.
What I'm saying is that there should be a way in MESS of specifying that a cartidge is one of the latter and should *NOT* auto-start. As I said I had done work on the MESS coco/dragon driver in the past that added an option for this, but somehow it has been removed which I feel is a backwards step.