If you press More Actions in the Upgrade tab of a weapon, companion, or frame, you can choose to swap polarities of mod slots around. For example, if slot 1 has polarity A and slot 2 has polarity B, and you swap them, then slot 1 would have polarity B and slot 2 would have polarity A.
Is this actually useful for anything? The only thing I can think of is that it might be useful to change the polarity of an aura/stance slot, but apart from that, it seems somewhat useless.
Elemental effects, and I'm guessing any other dependent mod effects although I'm not aware of any, are determined left to right, top to bottom. So if you want to have e.g. viral (cold + poison) and heat damage on a weapon, you need to have the first mod from the top left be poison or cold, the next be the second element for viral, and the third be heat, otherwise you would end up with cold or poison combining with heat instead. The uncommon variant of elemental mods have Naramon polarity for heat and poison, and Varazin polarity for cold, so for this example, assuming you only have these mods for adding elemental damage and you want to match polarities, you'll want to have an available Varazin slot from left to right, top to bottom before hitting your last Naramon slot. Thus, you may want to swap polarity slots if you want to change the order of mods to take advantage of the order in which they are applied.
Aside from situations where the order of the mods has a mechanical impact (mainly for determining combination elements), you may simply prefer to organize your mods in a certain way. For instance, I always like to have my weapon mods in order of base damage, crit, status/elemental, and utility, which makes it easier for me to see at a glance how it's modded.
If the item already comes with built-in polarity, or if I make a mistake or change my mind, re-ordering the positions may be necessary to get it set up the way I like without wasting time and forma.
