the reason the gear is lower ilvl is so they can match it later, "encouraging" you to re-farm that one trinket or w/e.
the gear itself being equal ilvl isn't really a problem as long as (and it ussually is) the gear from the raid is simply better and/ore more reliably acquirable for most specs, specifically in the trinkets/azerite/procs department.
raids simply require more effort to do than m+ and that should be reflected in the rewards in some (small) fashion. the ideal solution is that raids give the best raid gear, m+ gives the best m+ gear, and pvp gives the best pvp gear, but that seems like a unachievable utopia.