What about the possibility of buying some larger button "pearls" and just gluing them on top of the buttons you have? You could contour the edges with some fine sandpaper. The so-called "pearls" are available from several sources and in a number of sizes for euphoniums, tubas, and Sousaphones. Allied lists 13mm, 14.6mm, 15 mm, 15.5mm, 17mm and 17.8mm. Search on Ebay and you'll see all kinds. Votaw Tool Company also has some.
This approach would avoid any problems with the button not fitting or aligning properly with the valve cap. And I think if done carefully would not look particularly weird.
Tuba players -- for some reason lost in the mists of history, I'm sure -- have the habit of gluing coins on top of their valve buttons if they don't like how they feel or aren't quite in the correct positions. You could throw a few thousand dollars into antique gold coins for that purpose and you'd have a remarkable conversation piece as well.
Gary Merrill
Wessex EEb Bass tuba (DW 3XL or 2XL)
Mack Brass Compensating Euph (DE N106, Euph J, J9 euph)
Amati Oval Euph (DE 104, Euph J, J6 euph)
1924 Buescher 3-valve Eb tuba (with std US receiver), Kelly 25
Schiller American Heritage 7B clone bass trombone (DE LB K/K10/112/14 Lexan, Brass Ark MV50R)
1947 Olds "Standard" trombone (Olds #3)