Yep been masked by vision would be nice, but layers only happen on the DM side so if a player moves a token the DM has to move the layer. I do not see FGU ever getting player editable layer options, as this would basically give them 100% access to everything on the map hidden or not. It would be a massive/fundamental amount of work to create a player edit layer side. ( I'm not saying it will never happen, it could, but I've not seen anything about this option. )
Spell tokens have a small 'light' built into them, this is done to allow them to be part of vision ( as you say... ) but it also makes it possible for you to see them when they are not selected. Its a give/take thing, if it was not an aura and away from the player its required to help been able to select/move the player token and then be able to still see/select/move a spell token etc..
At the moment, spell tokens placed on the top of a player token, if you grab at the center of the player token both are ( should be ) dragged together. ( This uses a 25x25 grid area for the alignment and pair selection for the mouse hit box.. I'll make it 50% of the map grid size at some point, because if you run at say 100+ pixel grid size for the map the selection box to hit would be very small.. ) Depending on the map lighting settings this was not working on older FGU, but since 4.1.3 it should be fixed.
Let me know if you are having issues with this working or not ? ( as i say it could be you have high resolution maps and a big grid pixel size making the hit box very small, if this is the case please wait for an update. If you have issues on a standard 50 pixel grid map, let me know. )
I could possibly have an on-drop option, say 'hold shift' while you drop the spell token on map that disables the adding of light+vision... ( I'll add this to a my todo list.. )
I'm also looking into adding a option that while dragging a spell token about you can press a key (maybe ctrl) and it will add tokens under it to your target selection. ( I dont know when this will be added, but its on my todo list. Thinking spirit guardians auto moved with the player and the player adding more targets as he moves to apply the effect, or a 'dawn' spell effect that can be moved about when not near the player token and selecting to the use the character spell effect button to add the require effect to those targets. )
I'd also love to have a proper lighting masked spell token support, but its not possible with current API access.. All we can hope for is that getting this extension to a very good usable for player/dm side as best as possible, inspires FG dev team to extend the API or to 'fix' layers to a point players can put down ( FG spell templates ) layers instead of just the dm...
Hope this answers your questions, I'm always open to feedback/suggestions. ( But somethings are just not possible with the api access.. )
-pete