I suggest getting a valve length that is perfect fit for the shorter of the 2 wheels. Then, get a valve extender long enough to fit the other wheel.
For the flat kit, I use the thread on valve extenders, rather than the removable valve core version. I also have the extender already on the spare tube, because it is easier to remove than it is to install during a race.

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Alex Arman

Strava

2 spare tubes, one with extender in place. A few years back I had two flats at Hits Kingston within a mile of each other- won't get fooled again.

Exactly what I do

Seems like I'd rather do shorter valve that will fit disc only. Then the other have the option to put a valve extender on. That way forbid you double flat same tire you're ok.