I like when weapons become part of the alt mode, like many BW figures did. I don't care for the gun on top the the alt mode with the exception of ground combat vehicles. I also dislike pegging large weapons on to aircraft.
RTS Jazz gun and speakers hide inside. They dont turn into anything. He belongs in your second category
A few of Prime Specifically Ratchet, wheeljack, starscream, vehicon, kup, rid Magnus and a lot of the predacons
animated07 Jazz has some neat nunchaku that store as his exhaust pipes. and samurai prowl from the same line has his armor become his side car all god ginrai style. that's pretty sweet. also his ninja stars still peg into his wheels, which is always a plus.
The original Ultra Optimus Primal figure: 4 missiles, 2 swords, a flail, shoulder cannons and a wrist blaster. The original Deluxe Rhinox is amazing too.
In fairness all of them had pretty cool weapon intergration. It really was a hallmark of the entire Beast Era.
Tough but honestly, I think Siege Megatron's weapons forming the center and turret of his tank is the best execution of that idea, and T30 Trailcutter's shield forming the canopy in truck mode.
SS38 Prime has internal and external options in truck mode and in bot mode can peg to his back with dedicated side pegs on the gun.