Do not set limit in ppp profile.
Do that, and set up manual queues that only apply when going to outside servers so that there is still a general rate limit.
Or learn how to use queue trees to override simple queues.
Assuming a server with IP 1.1.1.1 that no rate limit is to be applied to, you can fake that out by overriding with a rate limit set to 100meg (or something else high enough to not affect clients).
/ip firewall mangle
add chain=prerouting dst-address=1.1.1.1 action=mark-packet new-packet-mark=override
add chain=postrouting dst-address=1.1.1.1 action=mark-packet new-packet-mark=override
/queue tree
add parent=global-in type=pfifo max-limit=100000000 packet-mark=override
add parent=global-out type=pfifo max-limit=100000000 packet-mark=override