I don't get this, is this really a technical issue or just an interface one ? It can be pretty clear to users that the semantic entity pages are very different from lexical entities in the same instance just by tweaking the UI. Or with separate instances this can be confusing as well if not well done.
Is this a community issue ? Different project, different communities, different site ? I really don't like it as it tends to make several groups who can have difficulties to talk to each other and go on the other site. I think as Wikidata community is already constituted and tends to try to grow and advocate for the project, considering its central situation in the ecosystem and that community tends to learn how to make interproject social links, it would be beneficial imho to continue to grow and to learn from here. There is strong connections between words and senses.
I think in that global scheme, one or several instance is a mostly technical detail that is not really important and that both solutions can accommodate to distinct (or not) pages or distinct (or not) communities.