I wonder how the cardiologist thinks your heart can tell the difference between 17 beta estradiol or progesterone molecules that have entered the bloodstream from your ovaries, or from exogenous gel or capsules.
I think a lot of cardiologists, particularly the older ones, still perceive HRT as dangerous and disapprove of it generally, believe they are doing the right thing by discouraging its use and will point to any symptom you have to do so - "palpitations? must be the HRT, better stop that". Similar conversations take place throughout the medical system "Sore ear? must be the HRT, better stop that". "Itchy feet? must be the HRT, better stop that".
If ovarian hormones caused arrhythmias, then surely younger women in their teens and twenties would be most affected.
Also if that were the case then the treatment for such conditions in a premenopausal woman would involve either oophorectomy or zoladex.
I suspect hormonal fluctuations are probably implicated more than the presence of ovarian hormones per se.
This may be able to be minimised by maintaining more consistent levels - have you tried patches or pills? I also agree that stable consistent lower doses of progesterone may be better in this instance than intermittent use at a higher dose.