I don’t think I can be of much help, but I will say that I run MainWP with 50+ domains on a simple $5 VULTR and it’s fine, so this isn’t an issue of the power of your server.
Most likely there is some kind of security feature blocking things. Whether MODSEC or a rate limiter or any other scanner. There is a lot of traffic between MainWP and the website, so this is a lot from one IP and you don’t want security tools to find it suspicious, so you may need to whitelist or something.
Something to think about.