I think these are both great furnaces you can't go wrong.
Modulating is every thing the two stage var. is and little more.
Make sure you get 10 yr Part and Labor warranty, because out of warranty repairs are going to be expensive with either.
If it was my house I’d go with the 2-stage, variable speed furnace and then modify it into a single stage to save on the gas bill. Longer run times with colder air just doesn’t seem like more comfort to me. I’ve even had customers who had their natural draft furnaces replaced with high efficiency two-stage, variable speed furnaces and they complained that they were cold. In both cases the furnace was keeping up and properly sized but their complaint was that the air coming out of the register when the furnace was running didn’t feel hot enough. Had it been a modulating then the air coming out of the furnace would have been colder yet. I should mention that I’ve only heard this complaint twice and both couples were older, like in their sixty’s and seventy’s.