You can modify Unreal Engine as much as you like to ship a game and the engine changes remain your property, you just have to pay their royalties.

At least that is how it is in practice - the language in the license agreement is actually a little fuzzy, when our game was sold from one company to our current one, the lawyers had a bit of a frowning session over some of the language there, but ultimately decided it was okay. Maybe in the future it will be challenged, but for now, self-owned engine changes are the norm.