I have already checked the location names and found no extra informations.
But maybe you are right, I don't recall there's a place that mentions the manor is exactly the same one. At least not in the main storyline. Although in the "Caught between love and adventure" senario, Vera told Gil that Lynx adopted a girl from a foreign country.
But think about it, in Chrono Cross, the Viper Manor also located far east of Termina, so it is not impossible Viper also built his manor far from the city in RD.
It is also possible that Viper had multiple mansions, being that he was a seemingly wealthy leader.
This previously posted image:
http://img.gamefaqs.net/screens/b/a/f/gfs_18926_1_4.jpgLeads me to this area,
http://i86.photobucket.com/albums/k99/eremes/vipermanor.png for a few reasons. Noted by the red and green dots, there are two mountains which can be seen to be similar areas in the previous image. One being the cliff the on which protagonists stand, and the other being the obvious black mound behind the manor. The "bridge" likewise could in fact be a large pier, as we see in my image, near the base of the lower settlement, which could very well be the crescent shaped city in Kodokami's image, on the right.
Now, due to the off-scale proportions of the original CT map, we don't know how big those cities, piers, or generally any of the topological data is. They could represent country sized settlements, or could all be one small city. This also means that the exact arrangement of the city may differ slightly in reality from that of CT's overworld map. However, there are three basic settlements in both images, both including a larger crescent shaped one, and two smaller ones diagonally across from it. From this information, what we see in the RD image, could point to the manor being in two places on my image, enclosed by blue and magenta respectively. Being that there is a forest around the manor in RD, those are the two most likely places I can spot on the CT map of 1000AD.
On the names Regiorra and Regionna... I have seen many engrish iterations, and strikingly many of them are in native japanese situations... To explain, I have seen developer's documents that write notes in english, such as for instance, the name of a place. When a third party comes to look at these notes, it is easily mistaken that Burger King is in fact Bunger Kirg, or various other falsities. This new name is then transcribed in either english or japanese, as the reader saw it, or, in the case of poor english users, when they write it and mistake a letter.
メ and ナ; ソ and ン; or さ, ち, and き, are all easily mistaken for each other, much like b and d, or n and r, or rn and m. It's quite possible Regiorra and Regionna are the same place, simply written by two different people.
To better illustrate:
Writer A notes : "Regiorra" on paper in english characters, for whatever reason
Writer B reads this accidentally as : "Regiona"
thus even the kana レジオーナ and レジオーラ both come to exist.
What say you?