Sorry, Surok... that won't change the /fx behavior.
The "players can use --ids" setting for TokenMod only applies to commands intended for the TokenMod script. When the script runs, it tries to make sure you have the rights to do what you're asking it to do to the tokens you have indicated. If you are using selected tokens, it knows you have access to control them, so everything works. The reason to need the --ids argument is to specify tokens that you *can't* select (there are other reasons that make it nice to have this argument, like being able to execute a command without having to select the tokens, but those are just value-adds; the necessity for it is to reach tokens you can't select).
Since we're talking about tokens you can't select, we're talking about non-GMs (or players). So this is TokenMod's way of letting a GM specify whether to let their players use this argument... but, again, it's *just* for TokenMod commands. It will not affect anything else.
I don't have a ton of time to investigate this, Ombres, but I think what is happening is a z-order problem with the effect. The "glow-charm" effect is sitting behind the token you "control", and it's so small that you don't see it because the token is in front.
To test this, try this command, instead:
/fx nova-frost @{target|token_id}
Target a token where the glow-charm command doesn't seem to work, and see if you see the frost effect. That effect will be big enough that even if you select a token you control it will expand beyond (at least beyond a 1x1 square) so you should be able to still see it.