In a recent island map game, i used transports to mount a naval invasion, this was a first for me.
The recruitment options for the skill/experience of troops as well as the size of their "unit" are both open to more strategic units like caravans and transports. I'm not sure why this is as its not clear to me that there is any advantage in either being more numerous or more skilled -unless they are attacked i guess.
Additionaly, I'm not aware of a limit on the transport capacity of naval transports. I was able to load my sovereign with 2 "parties" (of 4 units) - 9 units in total, onto a single transport.
Linking the unit size to some strategic or tactical benefit would make sense, otherwise remove the ability to recruit a "party" of such units.
The same should probably apply to pioneers, although i've not tried recruiting a squad of them.