I hate to just assume any shop/serviceman is "trying to rip you off" as a first thought, especially if not real familiar with the task...as in, if I was going to have someone fix my microwave or TV.
Did he mention what the "special tool" is & what he was going to do with it? A port-a-power, come-along, ect. could be needed (if for some reason you have bolted the cradle in the frame back on one side & forward on the other) to get the wheelbase even on both sides.
Not sure of anything else at this moment that would make sense. He didn't explain what the "mystery" tool is used for?
I just went through a wheel alignment disaster myself recently that still has me shaking my head. We fixed a 2010 Dodge 4500 4x4 truck with a toolbox bed & crane on it. We replaced the front differential (**Important** solid axle without lockout hubs or axle unlocking collar), the arms that mount it to the frame, steering box & all linkage...along with bumper, fender, ect.
I needed to send it to a shop that does larger truck alignments due to the length & weight.
I had the guy that fixed it drive it around a bit, he said it drove really well, but the steering wheel was crooked. So I drove it the next night to the alignment shop about 20 miles away. I left a note on the dash saying to do an alignment, mount a new LF tire on the new wheel (in the bed) & dismount the old one from the LF.
I get a call the next morning saying "I can't align it...It's stuck in 4 wheel drive & keeps kicking off the other head when I try to calibrate it." I assure him I didn't drive the truck 20 miles on dry roads in 4 wheel drive & not know it. I also mentioned that there surely wasn't a 4x4 light on the dash driving in the dark that I didn't see. His comment, "No the light doesn't stay on, it goes out with the other lights a minute after you start the truck." So I ask him what makes him think it's in 4 wheel drive? "Because I can see the driveshaft turning when I'm turning the wheel & it's making the otherside turn backwards while I'm trying to turn the driver's side forward." I try to explain to him that it's a new differential & may need someone to hold the wheel on the otherside. He goes on a tangent about "That doesn't work...years ago his friend on his truck, blah, blah & that the transfercase is definitely broken because when I go from 2wd to 4Lo it grinds like something is broken in the transfer case." I ask him if he had the transmission in drive while going from 2wd (across neutral) into 4Lo? His comment, "I'm not sure...I had it running, it may have been."
I politely told him to put the truck outside & we would come pick it up...feeling dumber that I spent 10 minutes trying to make sense out of this "kid".
Long story short...I send a guy to pick it up, the "tech" goes out in the parking lot with him & my guy goes through the gears in transfer case, light comes on in 4x4, doesn't grind going into 4Lo properly, ect. Guy shrugs his shoulders & said something like "It must have gotten unbound bringing it out of the building." & walks back in the building.
My guy drove it another 15 miles or so to another shop. They called me in less than 2 hours saying the truck was done. When the truck comes back, the damaged wheel/tire were still assembled laying in the bed...WOW! I asked for help on 3 things, got one accomplished....They either are going to have to get a new guy or not be in business.
Proceed with caution on your deal, but with an open mind. Lorne