From Prusa Woodworks, “Do you have space at the bottom of your mortise for extra glue?”
Well, usually, if it’s a shouldered mortise and tenon, I do leave space at the bottom of the glue, of the mortise for glue, just because otherwise, there’s, the glue tends to push the mortise, push the tenon out or the pressure of compressed glue at the bottom of the mortise. It’ll tend to push the joint back apart. In fact, even though we do leave glue well, what I call glue well, it’s about 1/8″ at the bottom, we were just putting a set of outdoor chairs together yesterday, and we had clamped it together, and as soon as I backed the clamp off a little bit, the hydraulic pressure inside pushed that tenon back out.

That’s because the epoxy that we’re using in that joint for outdoor chairs acted both as a lubricant to allow the mortise to move in and out freely, but also created an air seal so that the pressure of assembly created an air pocket at the bottom. So having a little bit of a pocket there for glue actually helps mitigate that somewhat. I don’t know that it’s absolutely essential, but for sure, you want to make sure that you’ve got at least as deep a mortise as you have a tenon, you never want to bottom out unless the shoulder’s what’s bottoming out.