Yes, if you run UBNT and Cambium gear on overlapping channels, they are likely to interfere with each other. Someone who has actually co-located UBNT and Cambium 5ghz APs might have more insight as to whether it's possible to get them synchronized, but to the best of my knowledge you won't manage that. Two ePMP2000 APs on the same tower can be on the same channel, since the GPS sync (if pertinent settings are the same) will keep them from seeing each other. (in principle two UBNT radios can also reuse a channel, though they never managed it reliably when I worked with UBNT sectors, a few years ago now)
If you're looking to compare their performance, you'll do best to clear a channel for the ePMP2000. If you are just looking to supplement and/or are planning to migrate to Cambium, then you can put the ePMP on a DFS channel, or a narrower channel, to start with until you are able to clear some spectrum.