The 1990 series isn't a part of the timeline. The only reason Supergirl is included is due to the upcoming crossover with Flash. While both the 1990 Flash and Supergirl were included in the flashes seen in the cross through limbo portions of the recent Earth 2 episodes of Flash, I'm not basing their inclusion only on that. Supergirl is firmly a part of that multiverse due to the upcoming crossover with Flash, but I don't view the 1990 Flash series in the same way because we're obviously not going to get such a crossover with that show from 26 years ago. It was just a fun nod/Easter egg, nothing more. ALL the other flashes seen (Grodd, Jonah Hex, future Green Arrow) all have direct ties to the existing shows (except the Legion ring flash, which may or may not be addressed in a future DC-CW show), whereas Supergirl and 1990 Flash show are different universes altogether. Supergirl's inclusion is due to the Flash crossover. The 1990 Flash series has no direct connection beyond the Easter egg nod.
The way I look at it, EVERY DC show potentially exists in some version of a live action DC multiverse for all the existing TV shows, but it would be ludicrous to try to force them all into a single cohesive multiverse timeline. Same rule applies to the 1990 Flash show. It wouldn't make sense to try to force it into the DC-CW timeline merely due to the nod shown in the limbo flash. And, as said, its completely unlikely (to the point of impossible) that they'll ever have a crossover between the 1990 Flash and the current version, whereas its a sure thing for the crossover between modern Flash and Supergirl.
So, I won't be including the 1990 series in the timeline.