With the inkan situation, we allow our customers to upload both their logo and their inkan. When printed, it looks exactly the same as a 'stamped' inkan. None of our customers have had any problems getting their MakeLeaps invoices processed, which is the important thing. For your interest, we have some printed samples here:
http://www.makeleaps.com/en/q-a/#topic-sending-by-japan-post