As long as the gap is unspecified, I don't think that's necessarily true. Just look at all the console Metroids of the last two generations. Not as if the X6-X7 gap couldn't use a bit of smoothing, though, I'm just saying they don't HAVE to do it.
Placing an Xtreme3 at any point after X5 would actually be considerably easier in terms of continuity than Xtreme2, since we're past the "landmark" of Zero's main-series interactions with Light. In fact, fitting between X6 and X7 hits right at the transition when Light went on an anti-social bout with X's supporters, so it would free them up a bit in that regard. As for X, just make sure the bad guy says something that stings him a bit at the end (I always saw the X7 "disappearance" as X6 Sigma's taunting getting to him).
Personally, if I did an X side-game I'd go between X4 and X5. I think a "bridge" story during that time period, after Repliforce and before Wily enters, would be very interesting to tell. However the Xtremes tend to be fairly self-contained.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)