Trane and Carrier are equal ,although I prefer Carrier because i think they offer more technical support and the schematics are easier to read .Is this a new installation or a replacement ? I need more info. on the flex such as does it run from the main trunk to the rooms it serves ? does it run through an unconditioned space - unheated. why is flex being used and not rigid metal pipe such as 6 inch round pipe ? I would buy the 2 stage and not the variable . because of the price diff. can't answer whether variable is more reliable but the 2 stage is reliable. As far as the flex goes if it's wire flex thats vinyl coated i would use that.It sounds like someone is trying to drive the price of the job up and confuse you with a lot of info.