While it is slightly counter-intuitive to me, form many years of playing, the way the Sadowsky pickup selector is oriented, it's hardly a problem to know that I am playing my Sadowsky, which means the selector is the other way. We all have different basses with different controls that we play, and that doesn't confuse us, so either should this. Put another way, if you have a standard shift car and a manual, you would not be confused-- you'd know which car you are in.
Totally agree.
On a related note: a few years ago I had a local guy build me a 5-string 1958-style Precision bass. It wasn't a typical parts bass because he carved the neck and body himself. The hardware was collected from various sources. Instead of the standard passive tone control, I decided to give the Stellartone Tonestyler a try. As an aside, the Tonestyler is a fun invention, useful to anyone who wants mid boost from a passive tone control, but here's my point: when I got my bass the Tonestyler worked opposite of normal: clockwise dark, counterclockwise bright. I asked the builder if he could rewire it the other way, but he said no. I should have realized this immediately, but eventually concluded that he had acquired a left-handed version (maybe on eBay, at a discount?)
As noted, in this case there was no option to rewire in the other direction as there is with a blend pot, but just as you said, it was easy enough to get used to the backwards control, and now it seems normal... on that bass.