With the allow activate extension/deactivate plugins, I am able to select the plugins that can be activated. I have plugins disabled which i sometimes use and then activate (less plugins, more security). Even thought the user may not activate or delete them, these options are available and work. For all activated plugins, this function works as designed.
Help with example in order I can reproduce your situation.
I made test with 8 plugins installed and only 2 active. Then I allowed user with read, activate_plugins capabilities in the role activate/deactivate only 2 plugins (1 active and 1 not active). User sees only those 2 plugins. Clarify on example, how he can work with other plugins. What I missed?