The MAKEOPTS variable content as defined in /etc/portage/make.conf is passed on to the make jobs launched from Portage and is most often used to allow parallel jobs.
The parallel jobs entry ensures that, when make is invoked, it knows how many parallel sessions it is allowed to trigger (when parallel sessions are possible of course). This is completely within the scope of that make command and has no influence on parallel installations (which is triggered through emerge --jobs=X argument). The recommended value is the number of your processors (or cores) plus 1. For example, on a quad-core processor, use: