They have nothing to do with each other, I just learned about an hour ago by RTFM. I was watching video and found there were still two compilers running at the same time, that got my attention.

For a year1, I mistakenly assumed that emerge -j JOBS would override MAKEOPTS in make.conf, the JOB is the maximum concurrent package emerging tasks, not the maximum concurrent compilation tasks using make command.

And MAKEOPTS is more than just for specifying the number compilation tasks -jJOBS for make, I should have thought about that, so I wouldn’t make a false assumption.

Anyway, if you want to override, e.g. I have MAKEOPTS=-j2 in make.conf, I want to keep one core (my CPU is a dual core) available for me, I run

[sudo] MAKEOPTS=-j1 emerge [options] atom

That does what I really want.

[1]I am just an one-year Gentoo user, 1 year and 17 days to be precise.