It's probably just for practical reasons, having Tycho not be Rogue Leader would require a second variant of Rogue Squadron specifically for that era, which would be fairly pointless, as it's a purely cosmetic change that doesn't really affect anything. Plus, during Era 1 Isard is already flying around in Lusankya (except in a specific GC), and in the book, Isard's taking off in Lusankya and the clearing of Tycho's name occurred almost simultaneously, what with Corran having escaped just a few minutes before it blasted off. Plus, if they used Wedge as Rogue Leader, they'd probably have to create a new icon for him to avoid confusion with the fact that he later commands Lusankya, which, to be honest, is already confusing enough, what with an SSD being represented by a portrait of a guy in a flight suit.
Basically, just like the original EaW, GC is an alternate continuity, where the course of events is almost entirely determined by your actions. For instance, the fact that Lusankya is flying around long before you have taken Coruscant in the progressive GCs is probably simply for the reason that Lusankya is much more iconic to Isard than her ISD.
If you're new to the mod, be glad you weren't around when it was possible to have two Thrawns in one battle, fighting each other to the death.
One was the IR version that appears during the Thrawn Campaign (era 2) and the other was the EotH version, which, due to Thrawn not being scripted to disappear from the EotH during era 2, could potentially stick around till the very end of a GC. And then, of course, you could end up with two Thrawns in the same battle on the same side, one being the original, and the other being the Thrawn Clone that appears in Era 5 in a Chaf. The enemies of the EotH were screwed enough when fighting one Thrawn, but two?