Hi arrjay, welcome to the forum.
My response to your questions are as follows:
First and foremost, most of the members here would recommend ordering your next frame from Peter at XMiplay, they are great to work with and have very good pricing. However, if you have established a relationship with another vendor that you feel comfortable with, order from them. As far as the frame goes, they should be similar. There have been some people making the claim that frames from Flyxxi are not as high quality, possibly seconds, and that's why that vendor is cheaper but nobody knows if any of that is true. They may just sell a lot of frames and by default just have more complaints.
Second, regarding your drop out question. In my experience, the only real advantage to the 12x142 thru axle for XC/Single track riders like myself is convenience of wheel removal/install. People can talk about flex and stiffness in a wheel but I believe they are imagining that the difference can be noticed in a thru axle vs QR. You are going to feel way more flex in the tire, rim and spokes before you ever feel flex in your axle inside your hub. That should clear up most of your questions.
When I built my two Chiners, did I go with thru axle, hell ya! Why, because I was buying all new parts anyway so why not jump into the latest standard. Since you have legacy components you want you use, just go with the standard QR and later if you want to get a new wheelset, upgrade your frame to the thru axle standard. If I were you, I would order an extra set of 12x142 drop outs as well as QR, that way you will have them for any future upgrades.
