You don't. There's a feature request for adding the ability to always try the primary DNS server first but it's still open.
When you configure multiple DNS servers in systemd-resolved, the resolver will assume all servers are equally valid and produce the same records. This is unlike Windows, which will always try the primary and the randomly try the secondary/tertiary/etc., or dnsmasq which should try the servers in order.
systemd-resolved will rotate through DNS servers, sticking with the one that works when the current server dies. It's not necessarily about speed, but rather about availability. If all DNS servers fail, it'll fall back to whatever fallback DNS server was compiled in by your distro (I believe Google's 8.8.8.8 is compiled in by default but you'll have to check the Fedora sources to see if they're configuring systemd for that).
You can install a DNS resolver that does take the "try every server in the list" approach after removing/disabling systemd-resolved. Make sure to update your resolvconf files to point to said server.
However, I do wonder if your Pi-Hole-then-microtik approach actually works on all devices. If your computer validates DNSSEC records, the fake results returned by Pihole will be discarded as broken, and your computer will probably try to resolve the domain on your router, undoing the blocking Pihole is trying to do. You'll need to disable DNSSEC verification for this approach to work if you're also including a non-blocking DNS server into the chain.