Well I kinda was replying to Aviemore, but I guess that doesn't really matter.
Honestly, I forgot about the Heroic difficulty. I thought they were removing difficulties or whatever. Like I already said the glad gate is kind of weird I'll give you that(lower the rating requirement), I thought they had a rating gate on each difficulty lfr/normal/mythic now you pointed out(I don't really know how I could've missed it) that they miss one and should create another one. If they want to create a system like this then you should be able to get equal gear in both forms of content.
Up until a certain rating the variable that matters most is skill, then you have the comp => gear. It can be skill>>>comp=gear maybe skill>comp>>>gear. But it will always be in that order. You can be as geared as you want and run the best comp of the season and still fail horribly. If you're playing at 1.5k rating and you think that lose because of gear then the only thing that can be said is that it is a l2p issue(1% power difference.) At 1.8k you have have a 1.5% disadvantage. at 2k and beyond it might be a little different and go up to 3% which still isn't all that much.
Back in 6.1 I started gearing my rdruid, with an ilvl of 680 in pvp, me and a rogue buddy with full honor gear managed to reach 1.6k without voice communication. Now we're both sub 2.4k players so we are not the best, it was in fact pretty easy even though the power difference was a quite bit more then 5%. Anyone who has ever invested some time into keybinds/setups and the like should be able to pass that. If not then you need to read some guides. Like with many things the small percentages only matter when you reach the limit of what you can do. You can play almost every comp to 2k. You can't play every comp to 2.4.
The reason they probably tuned PvE gear slightly better is because in the past it has proven to be easier/faster for PvE players to gear in PvP because raiders have lockouts, pvpers not. I think only the chance to get something is reduced after a certain amount of wins.
It's not perfect, but in the grand scheme and for most players(random bg's and arena's up to 2.1k) its a far more alt friendly system and a system that uses one gear set for both forms of content. Now rewarding the best gear for only gladiators is a bit much and they probably need another set of gear(hc) somewhere as well. But if you get beaten at your own content and blame it on gear which only gives you a 1 to 3% edge is weird. Now we're also assuming that most of the PvE players also do PvP, I personally only know 2 people who do mythic raiding as wel as pvp on a adequate level.
The only thing I dread and always will is the randomness.
I see your points, I understand why you're worried but I don't think those small percentages are that noteworthy.