One reason not to is becasue it would make dissassembly more difficult. As it is,. can remove the barrel while leaving the breech in place (and have to in order to uncover the breech screw). Loock the barrel and breech together and it will make sliding the barrel forward to get at the breech screw a lot harder. Don't think here is anything to be gained by setting the seal against the barrel, but if you've the urge to do it, don't see where it would hurt (other than making takeing it apart and putting it togeterh a bit harder).
If you just replace the transfer seal, have not had one of the poly seals leak or burst one me. You'll lose it in dissassembly if not careful, but they do not seem to wear out. If it doesn't leak, then it's done it's job....and they don't leak.