It already does that I believe (at least in a way). The difference is that there is a third mode in the combination settings called "none" which simply ignores that settable parameter entirely both when applying and learning the combination. It appears that OTQ2 will automatically ignore toggling a "none" parameter when setting a new combination setting (which makes sense--at least to a point). Whether or not ignoring a "none" parameter when using the set button is a bug, a feature that should be added, a preference that should be added, or something best left alone appears to be an open debate--that in the end only Modartt can answer. My vote would be for a fourth parameter which would act as a "soft ignore" or some kind, being none but reverting to on or off when setting a new combination.
That said, if you're setting combinations, simply edit the parameter to be either "on" or "off" instead of "none" in the "Combination" tab of the organ settings and it should capture/change them correctly moving forward. The downside is that you have to change that for all ten combinations on each organ. However, you can shift-click to select all monophonic couplers and the selection is remembered when clicking another combination setting in that window. The plus side is that you can use it to have combinations that won't overwrite parameters--for example, if you want manual control of all tremulants and the Vox Humana regardless of which combination you're using, you can set them to none and they won't turn on or off based on your combination changes.
There is a possible bug in that there is technically a fourth parameter I've encountered in some presets which can change around randomly. For example, when opening Baroque Church 1-4 today, the Grand Orgue 16' Quint, 2 2/3' Quint, Mixture IV, Zimbel, and Trommet all had blank settings instead of either on, off, or none. I don't know how exactly those blanks behave but they seem to usually be acting like an "off" parameter (and I couldn't tell if it's a UI issue, a combination issue, or a preset issue--I just know I'm running Windows), but once you click on those stops, it will only cycle through the correct three options. Also, when switching combinations in the combination window, these blanks stayed around but sometimes affected different stops. When changing their values away from blank, the preset didn't say it needed to be saved, so I'm not entirely sure what's happening there or why.
Spotify:
https://open.spotify.com/artist/2xHiPcCsm29R12HX4eXd4JPianoteq Pro & Organteq 2
Steinways, Grotrian, Steingraeber, Bechstein, Petrof, Blüthner, K2, Karsten, & Kremsegg
Casio GP300
