The Spaceways can use transponders 1/2 and 5/6 at identical center frequencies to the standard Ka plan transponders 1/2 and 7/8 . They may in fact already do so - aside from the information on Lyngsat which we know is not always correct (and in any case is wildly out of date) I don't think we know for sure what center frequency SW1 and SW2 use today.
Your objection would only matter for Spaceway transponders 3/4, and then only for the signal strength screen; for tuning a channel it wouldn't matter. To get around the problem for the signal strength screen, who says D14 and SW2 would have to overlap their transponders on 99s? Use 9-10 for the slightly offset frequency SW2 3/4 would be forced to use. Or heck, if SW2 uses different center frequencies for all of them, display D14 on 99s 1-8, SW2 on 9-14 and D11 on 15-24!