I've been quoted prices on shell and cxl, and it does appear that there is no upcharge for shell when I've heard it. That said, I wouldn't advise getting lined shell as a MTO
One of the great things about shell is how amazing it is unlined. IMHO, that's why something like the Wolverine 744 and 721s were so much better than, say, shell Indy boots. The lining takes away half the greatness of shell (as well as with CXL).
As far as my opinion on the upcharge, well, I'm not really a fan of it. It's fair that volume purchases should get much more attention, but remember they're not paying the same. If it's a standard margin, then a pair of $225 basic CXL boat shoes is probably sold to a buyer at $80-100 each, with several hundred pairs purchased. Rancourt gets the guarantee of the purchase, the buyer takes the burden of selling them and unsold inventory. So when Rancourt has this MTO option, they are getting the benefit of selling them directly, and getting that $125 markup to themselves. So, to say that they should get an extra $35-50 because of the extra effort is missing the fact that they are already getting that extra margin for themselves. That fact is even more important if its for a customization like baseball stitching or a different color CXL.
Right now, though, I wish that instead of a pair of Brown CXL rangers and a pair of #8 CXL boat shoes I'd just gotten 1 pair of #8 Shell rangers. C'est la vie though. Still have to decide whether my next pair will be shell rangers or shell penny loafers (probably the loafers, honestly).