Do you check for oversized gas exhaust flue in residential settings?

I have two opposing points of view from two chimney contractors regarding the size of the flue connected to both a natural gas water heater and a natural gas boiler. Together, the appliances add up to 145kBTU. The boiler (115kBTU) is fan-assisted but not high efficiency. The flue is roughly 30’ tall and 6" in diameter.

The first chimney company would not certify the flue saying it was oversized (and indeed it is according to the tables which call for a 5"), but the second company said they’ve never heard of a residential flue not receiving certification because it was a little bit oversized. They suggested the first company was scheming to bring in more business by requiring a rebuild of the entire system.

The way I see it, whenever a home has this configuration they are putting the water heater on the flue by itself all through the warmer months when the boiler is not turned on, essentially creating an orphaned appliance situation. So, it seems very common that a flue will be oversized, according to the code anyway, during some portion of the year, yet I never hear about this being a problem

What do you all think?

I agree with the second company, but the first company is correct too. This is not a home inspection issue, it is a code issue, and should be resolved by the AHJ if it is a concern. A flue liner can probably installed without having to replace the whole system.

If the flue is drawing right? If so, do not fix that is not broken.

No problems with the current set up. No corrosion, no signs of backdrafting. The township simply requires a chimney inspection before giving a permit to replace a water heater, even if BTU rating is same as old heater.