"Which would you go for ?"

Are you asking about choosing between the 700x35 or 29x2.2 wheels?

I'm pretty sure that both 700c and 29" wheels have the same size rims. I think the builder was saying it would take either one, with the 2.2 inch tires being too big for fenders to fit. (I don't know mountain bikes, but it appears that 29er rims tend to be wider than 700c road rims.)

I'd contact him and get more info. If the bike can use either size tires, it would work better with the correct tire for the ride, both on paved roads or on trails/gravel.

Is this a disk brake bike (which simplifies putting wide tires on the bike)? Sounds like a gravel bike?

~~~~~

I have a all-day-ride / gravel road / light touring bike. I'll switch between 25c tires (on wide rims, so these measure 29mm instead of 25mm wide), and knobby gravel road tires, 40c, depending on where I'm going.

Fenders
My 40c tires are a tighter fit with the fenders, so I tend to ride them without fenders, since mud or debris can build up in the space under the fenders, and I normally don't ride really wet trails.
But I usually leave road tires on the bike (not a lot of gravel roads around here), and then the fenders stay on the bike. In fact, I'm heading out this evening, it's 55F and the rain stopped an hour ago, but the roads are soaking wet. I'll be dry!

Rack
Your post mentions "touring machine". I have a lightweight rear rack that stays on the bike, and the builder added the frame mounting "braze-ons". The bike is set up for all-day rides. It's really nice to bring along extra layers, more water, lunch, even a U lock.

Tires
You weigh more than I do. A 2.2 inch tire is 56mm. That sounds great for off road riding, and 35c with a smooth tread would be very nice on paved roads.