They don't fit the boys in the tux when they measure them. They will just try on the jacket. When you pick them up, they try the whole shibang. At least that was my experience a few months ago when my 2 boys were in my brother's wedding (3y and almost 2y).
Im thinking the leaving out thing may have rooted from somethng in the past. They shld be coordinating with u and not with the kid directly imho. May get flamed for this but i think your ILs are actng weird.
To be honest none of this seems like a big deal to me. In fact, it seems to be saving you effort. it is weird that they seemingly ignored you when you were right there. My kids were just in my brother's wedding and my sister and now SIL picked out the flower girl dress without me (to be fair, my daughter was in the hospital so I couldn't be there anyway). I was annoyed at having to run around to get my son measured for his tux and to pick it up (it was too big so they had to order a different one and I had to go back a second time, definitely try it on!). To me, it was mostly a hassle so I say anything that makes it easier on you, go for it!
Re: moms of flower girls/ ring bearers