Yes, it's fine, since characters are identified by their realm. If you're going to be using ISBoxer like you say, then there's a realm field for you to fill out.
I guess there's the potential problem where you won't be able to trade anything between those characters unless they share a connected realm, but, no, other than perhaps some edge case situations where you're hard-coding namelists into add-ons, which could probably be fixed anyway if you knew Lua well enough.
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