What is the best codec for rendering a Rec.709 Master file in FCPX?

Don't use uncompressed. Unnecessary and you won't believe how huge the files are.

Most commonly users build sections in separate projects, then copy/paste into a master project and export. Do not render; it may speed up export a little but it's more likely to create problems.

If you want to go the route you outlined you can export ProRes HQ. It should be fine. If you want the best quality intermediate use ProRes 4444. XQ is really only needed for special effects compositing.

Anything above ProRes 442 (standard ProRes) is overkill and will give you larger file sizes without any benefit. Over sized codecs can't add data to clean up your video, it is what it is. Red. 709 is. pretty standard and even at 1080 a standard ProRes 422 file handles plenty of bit rate to do the job very well.

But have to have disagree with Tom, 4x4 and HQ are overkill, larger file sizes with zero benefits for Rec 709 HD. Especially at 8 bit, that's very little.

All the ProRes formats are 10-bit, or 12-bit. I think the higher bit rate is useful for multiple compressions at that frame size. That would be my choice. Because of the prevalence of 4K media I think that's why Apple made HQ the default render format, not that I ever render anything, but they still insist on having background rendering active as the default setting.

His media is 4K I think, which is why I’d prefer HQ.

Just copy paste. Compounds add a layer of complexity of you have to make changes. It also limits what you can do when you join the sections together.

You could export the effects heavy sections to simplify the master project.

HQ is still overkill for an 8 bit original, not matter the frame size. It's about bit rates and color space, not frame size.