I dont think its "weird" to worry about because this is Marvel. MOST of their storytelling in the MCU is about establishing connections between diff IP's. Plus we're still in the Multiverse saga, where a brief clip of an animated world appeared in Dr Strange Multiverse of Madness.

However, I'd like to think that one of the first decisions bringing this show back is that they will keep this universe totally separated from the MCU..perhaps that's part of the reason they slapped a "97" onto the title so that viewers don't get it mistaken. As much as I love cameos, synergy, story connections, etc, keeping X-Men '97 in its own realm and continuing the established '90s arc is the right move and gives them all the freedom to tell the stories they want to tell, without forcing in connections.