Everyone I am aware who have installed Right On Brackets have had no issues with bed alignment. The Right On Brackets are stronger than OEM if you remove the cross-member on the OEM. Plus, the guys at Right On Brackets are very accessible, members in here, and answer questions pretty promptly on this forum. If you call them or email them, they are immediately responsive. If you run across any issues with their brackets and your tonneau, I am positive they will work with you to figure it out.
No, I am not a paid spokesman for Right On Bracket, nor do I get any benefit from promoting their product. Their product was the solution to my problem, that problem being the same problem you are experiencing now with your MFT and chosen tonneau.
Seriously, if you have questions... PM RightOnBracket in here. He will answer your question.