Disabling Keepalive Timeout also disables MRU Test on RouterOS, since no tests are conducted, the MTU value never drops to 1480, a value picked by RouterOS when no Echo-Replies are received.
Yes, I also think these configuration should be separated, one should be able to keep the router sending PPPoE Keepalive Echo-Requests, without changing MTU value, even if large Echo-Request packets result in no Echo-Reply packet returns.