A little bit of gravel lost in the drain isn't going to be a big deal, nor a little space under the slab.
The flange should be glued and also secured to the concrete; you will want to secure the toilet bowl to the floor.
This might be a silly question but I've search and can't find an answer. I started finishing my basement. It was roughed for a bath by the builder. I read in a magazine the other day that sometimes the builder won't glue down the pipe for the stool so you can take it out and trim it easily. I wondered if mine was not glued. Sure enough it wasn't. So i wiggled it out and some of the gravel that was under the slab fell in the drain line. I picked most of it out then I stuck my shop vac house down it to pull what else i could out.
I'm not certain I got 100% of it. If there is any around the elbow it isn't much. maybe 10 pieces at the very most that aren't packed together. The gravel is about the size of three kernels of popped pop corn each. Is this going to be a problem?
also now when the pipe is in there there will be void around it from the gravel that fell loose. should i worry about that? it won't be very big. maybe less than one inch.
Installing the pipe that way is NOT a good procedure, because the average person, myself included, would assume it was glued in place, and a tight joint might also give that impression when the pipe was pulled on. There is NO reason to have to remove the pipe to cut it off, in fact the best installation has the flange slid over the stub, secured to the floor, and then the pipe cut off flush with the top of the flange. All done easier with the pipe secured into its fitting. Besides, if the system were properly tested, that "loose" joint would leak.