Perfect if the fee is taken from IPN message. So you’re right about no need of setting variable deposit fee.
About what I get when testing with 1 LTCT, here are some screenshots. In user balance is accounted 1 LTCT, as you can see.
According to this information, it is not clear for the user about how much he deposited and taken into account in his balance, in this case he sees 1 LTCT and 0.005 LTCT, but not clear if he got 1 LTCT or 0.995 LTCT.