Totally ok as long as you have enough real estate in the ear. Depending on the size of the kit you may have to adapt.
For internal record marking I have long considered a version of tattooing that would be similar to how mouse ears are marked: you have a code for each litter where you have a series of marks that correspond to a number based on whether they are in the right or left ear, near the base or near the tip, one mark or more. In this way you could do tiny dots, have faster, more pain-free marks, mark them earlier for tracking weight gain, etc, and on an adult they would be near invisible in the fur. I would not feel bad marking 3 day old kits this way, though my marks would never need to be higher than "12"....they would be able to be applied with a single poke per dot.
I never actually did it though.
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