Reality vs game need certain level of abstraction. On top, you need to make it so that rules are fun to use.
Mandatory knee on end of round is not fun. It is bad design.
As long as game do not have prone position (for simplicity reason) then kneel is only available "the_stable_position".
Because we don not want bad design of mandatory kneel for everyone, we need to find a group of weapons which has different usage, then grant this weapon group advantage over rest. e.g. special group of weapons has bipod.
As long as kneel is "the_stable_position" then we grant acc bonus for stable position to this group.
For creating a dilemma situation (Reaper is incoming, do I rather knee to get acc bonus or stand to get better melee defence ? )
it is smart to add also disadvantage for kneel in some situation. As long as kneeling is generally submissive position, and not very good suited for melee fight against standing opponent, it is very reasonable to set disadvantage to kneel in melee. There is no need for question "is it possible to fight on kneel?" . Of course it is(, with some disadvantge). The issue here is, make a rule which makes sense, is readable and is acceptable abstraction of an engagement.