To reply to myself again as I keep going down this rabbit hole, the opinion in Citizens Utility Board v. Klauser, 534 N.W.2d 608 (Wis. 1995) includes

Thus, the amendment as ratified by the citizenry only limits the governor’s veto of letters and keeps intact the Wisconsin Senate conclusion that the governor has the authority to “reduce or eliminate numbers and amounts of appropriations” and exercise a “partial veto resulting in a reduction in an appropriation.”

A “reduction in appropriation” is clearly not what happened here, but the distinction between letters and numbers is apparently, at least in the opinion for this case, intentional.