I think if you're "rolling your own" engine for one specific game, then anything goes. Though the "standards" nerd in me would want to make things as easily compatible as possible with external stuff like 3d models & meshes, textures and all the rest of it.
The benefits of using an existing engine, such as CryEngine or UE4 are pretty obvious, you can use standard tools to create content and assets, the vanilla editors are pretty good, and so long as you don't want to do too much that's not available out-of-the-box, development is relatively painless and good results can be achieved quite quickly (see original SC Kickstarter video

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