This can be conveniently accounted via Fast Travel time.
I did, for the sake of testing, run from Falkreath to Markarth one more time in SSE itself and timers are still correct.

Ports over the Real-Time Dragon Fast travel to Skyrim: Special edition.

Mod is save-friendly and can be safely installed/uninstalled during playthrough.

Dragons under the Bend will shout will now fly to a destination you pick on the map in real time … This file is just an ESP-ESL/ESPFE which contains a single game setting fFastTravelSpeedMult It can be safely installed or uninstalled mid-game. Changelog: It will change your fast travel time based on a very helpful "Skyrim Distances 2.0" …

This is actually a port from vanilla Skyrim.
Relative fast travel speed is not affected by in-game timescale if it was changed.