I think the point here is that the article should have said that Covid is between 7 and 40 times more likely to cause Myocarditis _for vaccinated people_ because unvaccinated people weren't studied.
No, because this study doesn't exist in a vacuum. The contribution is to quantify the relative risk between Covid and vaccines. We already know that Covid has a significant myocarditis risk on its own (as has any viral infection). On the other hand, the authors explicitly state they see no indication for an interaction after 28 days.
You are free to challenge the latter part, but so far there is no evidence that the vaccines "stay in your body" or something similar.
I think you might have misread the paper. Here is the relevant section about SARS-CoV-2 infections:
Amongst those with at least one dose, there were 3,028,867
(7.8%) individuals who had a SARS-CoV-2 positive test. Of these,
2,315,669 (6.0%) individuals tested positive before vaccination;
while 713,198 (1.8%) and 298,315 (0.7%) tested positive after the
first and second vaccine doses, respectively.
You are free to challenge the latter part, but so far there is no evidence that the vaccines "stay in your body" or something similar.