I agree that the difference you are aluding to exists, e.g.
"TrotzDEM
ich starke Kopfschmerzen hatte, bin ich zum Training gegangen."
(i.e. in the meaning of trotzdessen
, or obwohl
as you said)
vs.
"Ich hatte starke Kopfschmerzen, TROTZdem
bin ich zum Training gegangen."
(here you could use nichtsdestotrotz
instead, or also trotzdessen
, contrary to trotzdem
you wouldn`t make a difference in accentuation though).
The first usage however is quite antiquated and isn't used often in today's german.
As for a part of your question, if someone uses it that way (or other words for which such a difference exists), you'll probably catch the difference rather intuitively based on context and sentence structure (altough the differnce in accentuation is there too). I think catching it based on accentuation alone would be difficult (depending on dialect etc.) even for native speakers. I agree with @Emanuell's comment however that the it will sound weird in the first example if you use the second accentuation.
Right now I can't think of another (more modern) example of a word that has different meaning based on accentuation, but I'll try to think of something...