Considering that the RTA is around 2 hours 45 minutes (given I had to AFK due to an important emergency and reload some saves) but the IGT is at 1 hour 25 minutes, will this be invalidated as a run?
Not sure if mods will accept the raw footage from the Twitch Stream as is or they would pass a cut-down version of the run.
Ask in the forum for the game or contact the mods directly. Much more likely someone who knows the answer will see it that way.
Twitch Streams aren't archived forever. You'll need to highlight it, or download the footage and upload it to Youtube to make it permanent.
I would think you’d want to use real time unless it specifies to use the in-game timer in the runs rules.
As a general rule, loading a save made during a run is fair game unless the category uses in-game time, as reloading the save would result in gameplay not counted on the timing method.
Some categories may specify no save and quit or similar, which would also disallow loading a save.
One of the exception to that rule mentioned by @Ihavenoname248 are certain PC Games like the source engine games (Half-Life and Portal) that use demo recording and can therefore time those demos for in-game time rather than relying on a RTC like for example a Pokemon game would have.
I also would like to mention that usually RTA runs are done in a single sitting, so leaving to attend an emergency and coming back later would make your run segmented, which usually isn't a thing on here for humanly possible length runs, unless you kept the timer (in this case I'm guessing that'd be the ingame timer?) going and did not mess with it at all.
For exceptionally long runs (as in multiple days) some people like to have two RTA timers, one keeping track of the entire time and another that may be paused in-between to compare for how much of the total time was active playtime. Note that in any case only the total time (so the timer that never gets paused) is valid for the submission.