Both systems are comparable for how complicated they are for the player. You either lose a % if your current XP or all of your progress towards your next level. In both cases there is a player decision: do I risk leaving an obsolete unit in and try to grind the next promotion out before upgrading or do I pull him back and upgrade right away? But, if the next level is a floor for XP loss, the player gets to also influence how much XP they lose, so it will feel like the player has a little more control and that the system is something they can try to mitigate.
Without that level floor, a %XP loss is just a function of how many times you upgrade that unit. That means it will have a greater effect on unit lines that upgrade more often and less on ones that don’t. The XP loss on melee units will be consistent while this will have a sporadic effect on recon and mounted, who often dip in and out of usefulness anyways. Having a floor that players can use complicates that straight nerf in a way that players can work around, rather than it just being a straight nerf. Flat %XP removal also looks like it will favour civs with later UU unlocks, who have a power spike where they want to build larger armies later. Aztecs and other ultra-early UU civs have a fun mini game of trying to preserve their ancient elite regiments while still preventing them from being overtaken by the free building XP on new units. Any form of XP reduction on upgrade frustrates this, but with an XP loss floor you can at least reason that if you played better and timed upgrades well you could have kept your jaguars in action. If it’s a flat modifier players might feel they’re just being punished too hard for any of this to be worth it.
Im particularly interested/worried about what effect either implementation with this would have on the recon line. WRT your starting scout, a later ruin upgrading him could actually set you back, assuming ruin upgrades deduct XP too. Your starting scout will hemorrhage XP on upgrades for the rest of the game after the exploration phase is over, either way.