Depends upon the bike. Something with a basic mid-drive like a Turbo Levo I wouldn't charge more. But a bike with rear hub motor will definitely be more work. Especially since some of these DIY bikes are hardwired with no quick disconnects. You need to rewire the bike every time you remove the rear wheel.
Usually tine up include removal of wheels for bearing check and truing, so have to rewire a rear hub motored bike takes more time. A quick tune is just ck gears and brakes, cabled then yes same price as a HPB
Honestly, I thought we were talking mtbs and it never occurred to me that anyone would take a hub motor into the woods. But yes, the wiring involved with a hub motor would be an additional complication and thus and added expense. The same with anything homemade.....
I don't expect my LBS to work on my "home made" e bike, but I do take components into them, like the front wheel to get trued up, and my Rohloff hub built up. For one thing their bike stands can't handle the weight! Both our LBS's in my area are ebike friendly, while also being peddle bike hard asses, just good/more business for them and I'm glad to give it to them. Same on our trails here, no problemo.