Post-CD install: Software installation - website vs. gui vs. command line?

[unsolicited]

Post-CD install, it seems that sources.list is changed to prefer linuxmce package sources. (Good.)

Given that, is there any particular dis/advantage to the method of software installation - lmce admin website / command line / gui?

Is it reasonable to say if a bit of software isn't of concern to lmce, a package operates in the usual manner?

(I get that, for example, if I go and play with the network settings outside of lmce, lmce may well break.)

Gotchas?

Thanks.