This pipe comes up in the basement, right at the base of the stairs, too far into the middle of the room to do anything with; a closet around it would take up a huge amount of room. I think its the main cleanout? The cap on the inside is 11" below floor level. Can I cut the pipe flush with the floor and leave an access hole in the flooring that i put down? Not sure of any other options, let me know if you can think of any. We don't have a bathroom or sink or any type of plumbing anywhere in the vacinity. Thanks!
Yes you can, within limits. It isn't a pipe, it is a backflow device. The little cap down beneath the floor comes out to expose the flapper device which keeps sewage from backing up. When purhcased new, they come with a plastic friction cap to cover it up as shown in your pics. It'll allow you to flush cut it to the floor. The plastic cap can be covered with a metal floor escutcheon if you wish.
You can't install flooring over the device (and cover it up) however. They do occasionally require service or removal of debris, and they must be accessible for that.
Gluing the cap on it is not an option that should be considered.