Have used both, but mainly pucks on TM. Never could tell any difference in 2d picture quality, but then I "was" using the old school 2d units. Only disadvantage of skimmer on TM, IMHO ... size. That may translate into more chance of hanging the transducer into submerged objects. I don't think there's any difference in the internal workings of a skimmer or puck, just a shape change for each one to perform/mount according to where they're primarily intended to be mounted. The skimmer style is intended for transom mount use (speed), but can be mounted on TM with a specificly designed bracket. The puck is designed for TM use, but can also be used internally (thru-hull).
I can't relate to this situation now, with my current setup, as my TM mounted unit has a bullet shaped transducer encased in a sleeve bracket. It lays along the bottom of the TM, very close & tight (Elite 5DSI unit). My console mounted 2d HB depthfinder has the puck transducer mounted in the bilge flooring (internal).
... cp