if the top is fully electric, IE you press a button and it goes completely down on its own, including UNLATCHING, then yes an alarm can control it, however if say you have to LATCH the top once it comes up... then no.... it wont be fully automated, youd have to go out and latch it yourself....
alarms can control anything electrical, stereo on/off, windows up/down/vented (open ~2inches) lock/unlock pop hood/trunk (with solenoids of course) if you spend the money for linear actuators... hell even open/close your hatch completely for ya... (have yet to find cheap linear actuators to play with *grumble*)
Hope that answers your question
basically anything a relay can control, can be controlled by an alarm

if you plan on running lots of stuff off the alarm Vipers generally have the extender modules to add the extra channels, I cant recall another alarm that sells them or has as many channels.... *shrug* of course I havent looked recently...