When a plugin shows a <div class="compatWarning">, users asking to just install "all" updates should not get this one. (So something other than toggleCheckboxes must be used.) They should need to explicitly check it. Currently people are quite likely to install plugins which do not in fact work with their current core.
Alternately, the two Install buttons should show a warning dialog before proceeding in case you have selected one or more plugins thought to be incompatible with your current Jenkins version.
The same considerations may also apply to plugins marked with Compatible-Since-Version.