OK, I've decided to go with the cheaper of the two contractors.
Their guy came back a second time to talk some more after getting bits and pieces from the GF who was home when he did the estimate.
He didn't recommend a booster, but said they can put dampers in all of the lines to tweak individual room airflow accordingly.
His comment was that they are going to be limited by all of the duct and return sizes, in addition to the furnace fan, and that the 2.5 ton unit wouldn't net you anything but a clammy house. Additionally, he asked if they had quoted any additional electrical work for the 2.5 ton units. I said no, he said add $300-$500 because the current breakers would need to be upsized to 30 amp breakers.
He said the current t-stat location sucked, and that they would move it during the install to the master BR since we usually keep the doors shut (and this is true, it's usually scorching hot/freezing in the BR's compared to the hallway temperature, which overlooks a vaulted entryway).
He also planned on upsizing the return for the upstairs, which he said was marginal for the current install, and would help quiet things down some.
When asked about equipment, he said that he really hates Goodman units and isn't a fan of Lennox and SOME Trane models just based on parts availability. When asked about Heil, he indicated that you could take the name plate off the equivalent Bryant unit that ISC manufactures, and would never know the difference.
All in all, the guy seemed to know his ****, said there would be no extra charge for the dampers/return/relo of the t-stat (said they pay me salary, not commission), showed up on time, returned phone calls almost immediately, and the guy doing the estimate also heads up the install.