The big advantage of free-cutting EN1A is that it machines well, ie it's easier to get a good finish while taking less time to do the cuts. It's common enough in rods, but I've never tried to buy 50×50 square, which does seem hard to find.
EN3 is a little stronger than EN1A so it's suitable for what you need strength-wise. But EN3, which is cheaper, doesn't cut as cleanly and it's harder get good looking results. As Andrew says, it tends to tear.
Apart from a slight difference in appearance, there's no functional reason why you shouldn't use a mix of EN1A and EN3 for the tools. Free-cutting EN1A wherever you can get hold of it, and EN3 for the awkward sizes.
If appearance matters, listen to someone else! As I'm an experimenter rather than a model maker I rarely worry about the look. Provided stuff fits together and does what I need, that's OK. My advice may be anathema to the chaps who make wonderful stuff that works AND looks beautiful.
Dave