Most of the references I've seen is about setting launch options in the properties, but when I launch the game launcher I can just select the mods and even set a pre-set profile for the 506th mods.
It shouldn't cause any issues. That's what I have been doing and it has been working fine. I've completed Recruitment training, OSUT days 1 and 2 as well as some fun missions with no issues.
I use the launcher that comes with Arma 3 too. The only problem I've had is that sometimes when I start the launcher no mods will be selected under a given preset and the name of the preset will have an asterisk next to it like I had changed the mods and forgot to save. All you've got to do is re-select the preset and you're good to go.