People will do what I plan on doing, putting junk lvl' mods on junk toons you won't ever use in a combat mission and park them. Why unmod them?
The only swapping useful will be between a few teams used for the special, combat missions and the 10 or so toons for Playoon so locking the mods won't affect Deployment score than any more than 1k per toon used in those. Maybe max 20k per phase. Given its millions between star levels esp the higher phases you are in, it would very, very rarely make any impact what so ever.