I've never had that done, but I'm pretty sure what they do is take the board out of the cartridge case and put in one of their boards with the burned EPROM chip. So you basically just get a repro inside your original cart shell. As for rights issues, there are always rights issues when someone wants to raise them. If someone wants to be enough of a dick about it they can make the case that even translating a rom is illegal.
In other news...
Advanced Military Commander
UGC cover: http://www.box.com/s/yof1ggfydaipaem2gkht
Sega clamshell cover: http://www.box.com/s/i2audvdfq6hjoybxofnh
Cart sticker: http://www.box.com/s/u90qnu0bpp5dn6ij5ym9
UGC cover: http://www.box.com/s/6rypgo00ec0d5q7ja11g
Sega clamshell cover: http://www.box.com/s/vqyptqf24melme0ph31j
Cart sticker: http://www.box.com/s/m16u2zf3ejl90gb6cp1g