Very much welcome to the Forum!
I can't imagine the shapes of bases would be a problem for anyone you'd ever want to play against. As a strict 100% fantasy player I must of course applaud your final decision on that one..
On the other hand, given the fact that Fantasy is predominantly played on "movement trays" it'd be pretty easy to rank up round bases where-as square bases in 40k is always going to catch the eye.
Oh look at me playing the devil's advocate.. Of course the bases should be square!
"It's hip to be square!" - simply put!