I considered making a post just like this but then I tried the gabled SEARCH functionality.
I have some of the same concerns as the op, but my argument is one of balance rather than realism.
I've also skimmed through this thread again and it seems to me most of you think the rules work well as they do.
But right now I'm about to play a module where the enemy is supposed to have autoguns, revolvers and axes. Now 1 out of 3 here it primitive. Although they are supposed to be menacing, in fact they are ridiculously bad because the PCs non-primitive armors means they can easily shrug off most hits from axes. Is this realistically? I don't know, 40k isn't realistic. Is it balanced? Well axes are fairly cheap, but melee weapons suffer a lot of disadvantages already. The worst part is "is it fun?" I can allow alot for the "rule of fun" or "rule of awesome", but although It could be cool if the attackers rush into melee as soon as they can there is no mechanical reason to do so.
I know the arguments, a knife should have little chance against 40k armor. But people fail to take into count a few things:
1. Armor is not all-covering. Even Guard Flak has alot of weak spots if you look at the fluff and pictures, if nothing else the faces are completely uncovered. AFAIK, only Power Armor is all-covering with no unarmored points. Thus is should be possible to jam a dagger into the face of a Guardsman and kill him. By RAW this is impossible without divine intervention (also known as Righteous Fury, which almost no people are entitled to).
2. Primitive weapons are ubiquitous. Not even counting Feudal planets, it seems common for soldiers and civilians alike to drag around swords, hammers, axes etc. that are primitive. Why do so if most cheap common armor makes these weapons useless? Why isn't Mono upgrade standard issue?
3. In real life a sword has no chance of actually penetrating plate armor. It could potentially find weak spots or maybe slip through a crack somewhere, but to actually penetrate it you'd need a great weapon or a fast flying projectile. Even so plate only give 5-7 armor vs primitive melee weapons (the latter being best quality full plate), while even normal quality guard flak armor, gives better armor than that. So even if Flak is much better vs swords and daggers than Kevlar is against sharp objects in real life, why should it be DOUBLE? Isn't it enough that the armor work just as well vs swords and spears as it does vs bullets and las bolts?
Therefore I suggest this simply house rule:
Primitive armor works only half as well against non-primitive weapons (as normal). Non primitive armor has no special advantage against Primitive weapons.
To compensate somewhat, the Mono enhancement is gives either Penetration 3 (instead of 2), or +1 damage.
Now how do you think this would work? I think it would change little except that the PCs would be more vary about letting goons come close to them with melee weapons. Primitive ranged weapons are already so bad that they have a hard time damaging people with ANY armor. For instance, crossbows has 1d10 damage which is consievably less than a strong man with a dagger and Street fighter can do. An acolyte in my group was attacked by 20 ork archers for 3 rounds, and despite my ad-hoc rule letting some arrows do damage unaffected by armor, he still was a more or less lightly damaged pincushion at the end of it. Ridiculous.