The Heritage Foundation can say whatever they want about SpaceX-- just because they can say it, that doesn't mean that SpaceX as an entity is onboard with the position Project 2025 paints for them.
It's true that some people connected to SpaceX were also interested in missile defense, but that's hardly unusual given that we're talking about the intersection between defense and the aerospace industry.
To the extent that SpaceX enables missile defense it's in the same way they enable any other space endeavor, as a natural consequence of lowering the cost of lifting payloads to orbit.
Trump has been pitching a reboot of Reagan's Strategic Defense Initiative using Elon's Starlink. At least publically since his reelection campaign: "the United States will build a missile defense shield to intercept nuclear weapons" https://www.dailyrecord.co.uk/news/politics/donald-trump-pla... It's also in Project 2025 / Heritage Foundation docs.
SpaceX was founded in 2002 with help of a CIA agent named Mike Griffin ( https://en.wikipedia.org/wiki/Michael_D._Griffin#Career ) who funneled them funding (lots of citations at end of https://archive.ph/D2zIG ). Griffin worked for In-Q-Tel and also was the Deputy of Technology for the Strategic Defense Initiative, later started the Space Development Agency (SDA) which is to become Trump's SDI in 2025.