Considering that you are looking at the 80% efficient gas fired unit it's all the more reason it's critical having the correct sized liner. The one estimator was correct for the reasons that JLMCDANIEL and JacktheShack outlined in their posts.

The one thing I would add is to consider having a stainless steal liner rather than a galvanized one. Depending on the building code in your area it may be a requirement to have the stainless steel one anyways. The exhaust gas will be moisture laden and somewhat acidic which will eventually rot the galvanized steel liner. There will likely be an up charge but depending on how long you will be in your home it's worth it.

If the second estimator didn't have a clue about this my recommendation would be avoid that company.