Jeff,

You have your wits about you..., yes through tenons and even pegs should be trimmed or driven (pegs) so they are less than flush.Though I will sometimes allow a through tenon or a plate to flow on out into the enclosure system. Traditionally Timberframing was and some would say is properly "green" woodworking.

The same thinking should be carried on into your joinery, extra mortise depth so tenons will not bottom out as the frame seasons, an extra moment paring at a knot so it will not stand proud and force a joint apart, etc. etc.

Your trunnels should be tapered if you are draw boring, and you should be (in my humble opinion) if joining green timber.

Yours is the best case senario for going green, winter cut timber stuck up for a yr (its amazing how much winter and a yr will drop the moisture content in softwoods)locally milled timber in the teens %age range. Good on you