They are thinking of settling on a rheem
Condenser Model # RP1636AJ2NA (two stage 16 seer )vs the bosch. They based it on bosch availability for parts and their overall place in the industry right now compared to other established brands.
Why a 3 tonner for a 1 ton cooling load? (= crazy, even if 2-stage) The RP1636AJ2NA is a woefully low-capacity low efficiency piece of crap in heating mode, with a max capacity of only 21,600BTU/hr @ +17F, per the table on page 15 of the manual. That's a heluva lot less than your ~26K+ calculated heat load, and WAY more cooling capacity than your 1 ton calculated cooling load. (The output of a 1.5 ton ducted minisplit with a cold-climate type compressor, or a 2 ton full size air handler version would be comparable to the output of that 3 ton Rheem. Just sayin'...) Who cares if it's a 2 stage if it's undersized for the heat load at max rating, and (probably) more than 2x oversized for the cooling load it it's low rating? Keep shopping.
The Bosch BOVB-36HDN1-M18M / BVA-36WN1-M20 (made by Midea) would at least come close to covering your heat load, and would be able modulate down to something like your 1% cooling load. It would still cycle more than it modulates in cooling mode, but not short cycle. Overall it's a much better fit to your load numbers than the Rheem, but an even smaller higher efficiency version is probably better.
Id love the idea of a mini split but the ductwork system is based on the old 10 seer unit for a 1.5 story ish place the room configuration is also an issue - after looking in the basement whoever did the ductwork did a not so great job ill have to get a couple steel elbows and a flex duct or two, theres like 90 degree short bends on at least 3 of the runs- its turning into a hot mess. i was going to see what toaster they had originally but my list had a 10kw in mind. Time constraints/financing and the weather are likely affecting this decision
It doesn't sound like your ductwork could even handle a 3 ton 2 stage 16 SEER unit. What's the rated cfm (and blower motor type) of the air handler they specified?
The smallest unit that fills the bill will have a lower cfm, generating lower static pressures. I suspect the 3 ton air handler is rated for ~1200 cfm @ 0.8" or 1" w.c., whereas a 2 tonner would be <900 cfm. That may not seem like a huge difference, but it is. Bear in mind that the static pressure rises exponentially (third power) with duct velocity. On a given duct system the static pressure at 1200 cfm is more than twice the static pressure at 900 cfm.