As can be seen above, you'll find a split opinion on this. If the tenon fits well and you can, it is fine to clean with the stem in. If the tenon is short, you'll get funky buildup in the mortise from doing this. If the pipe is a system or has an extreme bend, you'll have no choice but to remove the stem, depending on drilling and such. If you run filter systems you have to remove the stem. It kind of depends on your own comfort and the pipe, but you will want to occasionally remove the stem and deep clean in there regardless.