I'm contemplating doing similar (just to have something to play with).
You should not have any different issues than you would using one RPi for both. Simply create two different profiles and use the appropriate one. I'm currently doing that with both of my RPi's. I have one targeted towards use with the NexStar 8se, and then another for the William Optics ZentihStar 103mm. But I have profiles for both on each one... and the WO has 2 profiles, one for use with the ASI585MC and one for use with the ASI533MM.
The only question may be since both mounts are of the same "family"... does each profile keep it's own settings for said mount configs.

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