This is unlikely to be a problem. There are many companies that have already registered software-related trademarks prominently involving an
X or the name
Xcom. That Twitter has changed to
X branding does not substantially change this general situation.
With trademarks, the general question is whether similar branding causes confusion. It is unlikely that someone would confuse the X display server / X.Org project / X.Org Foundation with the social media service now being branded as
Of course, anyone can sue anyone, the real question is whether that's possible successfully. Here, I have my doubts that
x.com could successfully demonstrate confusion in its favour.
It is worth noting that the X.Org Foundation does not seem to hold any relevant trademark registrations at all. This is not unusual for Open Source software projects and doesn't mean that X.Org has no rights, but does make a defense a bit more difficult. However, there also doesn't seem to be a relevant registration by the ex-Twitter company or by the X Corp.
x.org domain name is unlikely to be threatened. If the
x.org domain name was being used in bad faith it could maybe be seized, but the X.Org Foundation has a pretty strong claim on this name. For historical context, both
x.org were among the six single-letter .org/.net/.com domain names when such registrations were stopped in 1993. But while
x.com has been pretty much dormant since that company was renamed to PayPal,
x.org has (I think) always been associated with the display server software, and has been used continuously by the X.Org Foundation since its establishment in 2004.