Shadow to Clyde Arrowny in end credits

Was it confirmed that Relm's last name came from her father and not her mother?

Normally in Japan the children of unmarried couples end up with the mother's name. There is also a HUGE social stigma in Japan for women who have children unwed (hence the cultural assumption that mothers are going to be wed, at least in some manner).

We know that Relm's mother lived in the same house Strago and Clyde did (though yes, there being no 'empty houses' is more due to hardware limitations of the time, and there is only one NPC spreading rumors that Relm and Strago aren't directly related, but the fact that, if Strago is not related to Relm, the fact that he took possession of the house and the kid after the mother's death would be drawing attention in its own right in such a small community, whereas multiple generations of a family living in the same household would not draw much attention at all), we know that the mother died at some point years after giving birth to Relm, we know that Clyde had been there for a long time (long enough for Relm to speak and realize her father was gone after he left (so she was likely four to five years old at that point), we have the above contexts I just pointed out regarding Japanese cultural assumptions regarding mothers, and we know that Relm does not have Strago's last name of Magus (which is likely the shakiest bit in the entire chain of details we know). We also know that there are extra details that were released in japanese-only data-booklets.

Given all those details, it's more likely than not that Relm got the family name "Arrowny" from her father rather than her mother.

Beyond that, I would ask Djibriel and Imzogelmo, as they could likely fill in any missing info I haven't already covered. So while you're right that it isn't "100%" confirmed, given the contexts I'd say it's about 75% to 85% likely to be the case here.

There will always be some uncertainty due to the fact that "Clan" and "Social Rank" is also a factor to Japanese culture (meaning Clyde might have taken the mother's last name when they married AND Relm got her last name from mom at the same time, or other variations and themes along those lines), and with the game developers being from Japan and not being directly upfront about some things, well...