So Fryette's approach and philosophy goes against most of our understanding on power amps/tubes and their overall effect on the tone. If you search his thoughts on the subject, he's gone into it a few times. The gist is the circuit is designed around the tube that it's intended to use; the tube doesn't dictate the sound, the circuit does. He designs his amps to be pleasing for guitar tones, so not flat but an appropriate curve for guitars. That's why he was the designer of the Synergy amp because it makes the most sense for this platform where many different preamp tones need to translate (and he already had a 1u power amp design).
I'd speculate his designs have tight tolerances hence only able to use a 6L6 where something like the RT2/50 can accept a broad range so you get a lot of character but at the expense or benefit of coloring your tone.
I don't have the SYN50/50 but I'm curious how it would compare to my 2502. One thing the 2502 has the 5050 doesn't is the voicing switch which I find very useful, especially when trying to get the right tone in some rooms.
I'm not sure how much I would be concerned about the tube selections impact on tone for the 5050 as much as knowing it a more reliable selection. Power amp tubes really are further down the list in the overall variables that affect your tone. Now speakers...