How is it changing the original design if you are using the same tube type? Most equipment is shipped with generic, crappy new production tubes. The company often lists alternatives, or upgrades, and encourages people to try them. How is that any different than tube rolling or am I missing your point?
That generic, crappy new production tubes in the unit are the same tube that the manufacturers, in this case AVA do their bench test on before they ship it.
I doubt that Frank has a set of gourmet tubes there only for bench test purpose, or after the unit passed the bench test, he stuck a pair of generic, crappy JJ tubes in there, then ship the unit to you.
Substituting tubes with different made, with different manufacturing method, with different response curve is altering the original design. You would hear the difference, better or worse is all psychological.
Tube rolling is similar to putting magic caps in the unit by the customers, but not as bad, at least same type of different made tubes won't screw up the circuit, but keep doing it may wear out the tube sockets, it will keep them clean and shiny though. Tube rolling will also increase the chance of damaging the unit. Most people end up leaving the cover off with the unit on, then dropping something in there while the unit is hot. Or keep taking the cover on and off, end up stripping the chassis sheet metal screw holes or the screws. Bad idea overall.
As far as for "the company often lists alternatives, or upgrades, and encourages people to try them" part, it's a selling pitch. It gives the customers a sense of empowerment, it makes them feel like they are in control. Actually companies recommed to purchase tubes from them because their tubes might have been matched and tested in the factory, so using them will increase the probability of operational success.