A day in Top Eleven is like a week. You have league match each day normally so I suppose it's a week in game time. (or even more if you take into account that 1 year is 54 weeks and a player gain +1 on age much sooner than in 54 days real time)
So, is 40% condition/week good? Probably no, it should be 100% or so in order to be more realistic.
But, I get your point, even in 1 day you can train your players lightly so it's sure enough 5% every 3 hours.