the thing about fibula is that eggman didn't pick him to be his guinea pig for necromancy for a reason. literally, he just randomly chose a grave to rob. fibula wasn't special... he just got "lucky." for the first time in his life. and isn't it ironic? this guy, who spent his whole life working so, so hard... for nothing... falls into the hands of a supervillain Just Because.
it's like spider-man, but twisted. you know?
and while fibula is mostly indifferent about eggman's cause, he pretty much instantly gets attached to eggman himself. because he's the one who gave him this second chance at life--without even being asked. it's the only time someone has ever offered fibula something so meaningful, and he holds onto it with all of his undead strength.
so, yes; fibula owes eggman. but he also just wants to prove that he deserves this second chance. to make eggman proud. because that old hardworking, people-pleaser attitude that fibula carried with him all his life isn't truly dead... it's just found a new source of motivation.
and the best part? eggman DOES appreciate fibula... for what he can do for the empire. finally, someone sees worth in him, and it solidifies his loyalty to a man who, in life, he certainly would have despised.