If you want to get really technical, the Jugdral games (FE4 (Seisen no Keifu/Genealogy of the Holy War) and FE5 (Thracia 776)) are stated to have taken place in the distant past of the Archanea continuity
Really? I didn't catch that. I know some people have claimed that Ike's games take place long before Marth's, but I understood that it was just an implication rather than something confirmed... But yeah, if TC wants to play the games "chronologically", probably the safest way to do that would just play them in the order they were originally released in if possible (except BS Fire Emblem and GBA Fire Emblem, which are both definitely take place outside relase date order).
Loptyr is from Archanea, (Note, FE4 specifically takes place 400 years before the kindgom of Archanea was founded), there are some story and in universe calendar hints that show this. Also, the Naga in FE1/3 is the same character as in 4/5
Timeline of FE1 through 5 (and Awakening), spoilers ofc. http://fireemblemwiki.org/wiki/Timeline_of_Archanea,_Valentia_and_Jugdral --- 3DS FC: 4596-9460-1427