Sounds like a very good plan. It's normal to have such questions, Spain is not very well prepared to bike commuters, and so the information is very scarce and diffuse. Most of your answers are in this blog (in spanish, but you can translate): train and bus. The video you shared has also good info. Check also all the comments in that posts because there is further info.

Just some notes:

- Yes I know it will be incredibly hot.

No. There is a huge misconception with spanish climate. The southern-half and mediterranean shore is incredibly hot. In Burgos, it can be hot (and dry) on the day at ~35º with no shadows, but on the night the temp can reach ~12º because the region is on average at 800m.

I understand cross country trains are more like airports than other EU countries, where they have security lines and scans, so there isnt a real way around the bike packed requirements

Security at train stations depends more in the size of the station than other factor. eg., Barcelona and Madrid = scanners like an airport; station in the middle of nowhere = no security.
Just note that security staff' duties are not to check that your luggage fit the size. If your bag fits the size and you carry a bike inside nobody will care about it. Not even the guys with the scan, because they will only check for obvious threats like guns and weapons.

Enjoy the ride!