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All 700c rims will technically be compatible with the bike, its the amount of fine tuning that may or may not be needed to allow 2 different wheelsets to be 'hot-swappable'. Even within Shimano, RS10 rim dimensions are likely to be quite different from say an RS80 rim. You can try looking up the external rim width and height of the braking surface to determine how close 2 rims are, but not every manufacturer will list this info. Keep in mind to look for a Shimano/SRAM freehub, the Campy ones are different.
As for rear cassette gearing, you should be fine on an 11-25 with a 36-46 front. It all depends on how you find your gearing now. If you find that you run out of low gears, it may not be the best idea to move to an 11-25 since your lowest gear will be harder than with an 11-28. If you find you are never in the first and second low gears anyways, then you can move to an 11-25 and lose nothing, but you'll gain tighter and more consistent gearing. Since your high gear stays as an 11, you're not going to gain or lose anything on the high end. I run an 11-28 because I'm using a standard road 53-39, and I need that 39x28 low gear. Having such a large spread results in a slightly larger gap in some gears than I would prefer to maintain a consistent cadence, ie. one gear feels too easy but the next one up feels slightly too hard
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