I haven't seen season 3 (yet), but I did capture two moments in S03E05 (towards the end) and E06 (at the very beginning):
In this second shot, it becomes more obvious that the white hazmat suits are actually grey (the two guys in the center are wearing the suits with the masks taken off):
I think the different colours could simply indicate levels of protection:
Here, grey and burgundy are at the extremes on both sides, which doesn't make sense in the scene of Stranger Things, as people clad in both colours are working in the exact same environment, their suits being visually completely similar.
The only remarkable difference - apart from the colour - is that the burgundies are the only ones interacting directly with the plasma gun.
I believe therefore, that the colours must be either indicators of levels of proficiency or specialisations.