Thank-you letters sends email immediately
I think there are two issues at hand here:
CiviCRM does not use the CiviMail/it's mailing feature for the thank you letters. In many case that would make a lot of sense but I guess when the feature was built no one considered using it for so many emails. You may use another extension that sends contribution receipts via CiviCRM's mailing feature such as this one: https://github.com/systopia/de.systopia.donrec
The other issue is that you should probably configure your mail server in a way that it is less likely to be classified as spam. There should be many questions &amp; answers regarding such configurations here on Stackexhcange, most important would probably be so set up proper spf records. This will not necessarily solve the problem described above (e.g. Mailer Batch Limits or resource usage).