If you make the trunnions as one pice with the barrel, the grain would be oriented worse for shear stress than if you made seperate trunnions and glued them in. Of course, with the meager loads you're thinking of using, I don't think this would be a big factor.
It would be possible to line the trunnions just as you are lining the bore, press fitting or screwing them into the liner. I'm not sure that would be worth the effort.
Addressing the trunnions or not, I can't see why you'd go through the effort to install a liner to shoot it once, then remove the liner. If you want to do that, just shoot it with the wooden bore starting at really small charges and with sufficient fuse length to be well out of range of any splinters.