I would go with what the manufacturer recommends. Larger might cause the exhaust to cool too much, resulting in condensation.
I agree on the larger gas may cool the vent and cause condensation.
I am currently in the middle of the install of a 45,000 BTU Sterling Garage Guy heater (pictures will follow in a future thread). I am doing this on my own for this job, and I am slowly getting it up (it is mount to the ceiling now and properly supported and structured. I just finished the rough in of the flu. I just have to seal the connections.
I recommend the Simpson B-durvent line over the Selkirk kit that I bought. Everything just seems more thought out in their attachments and slip together design. Selkirk (at least the kit I bought) still uses screws in some places (top vent cap), and the kit really wasn't complete at all. What a pain. I used B-vent for everything, even 90's
I am just doing regular and not separated combustion for the time being for my sterling. I may in the future order a concentric vent box if I can find one cheap enough online..... or I may just vent the intake combustible air to the outside from a side wall. It says nothing about doing this in the instructions, but I think they just want to sell you the expensive concentric vent box.
On thing, it is weird how Sterling recommends 4 inch venting, Mr Heater recommended 3 inch vertical and 4 inch horizontal venting, and it appears that Hot Hawg wants 3 inch for both horizontal and vertical applications. All different recommendations for the same 45,000 BTU type and style of heater.
Kinda weird, but in this application, manufactures instructions are made to be followed for good reasons.
Ryan