That because for the ethernet port auto-negotiation is mandatory for 1000BASE-T and faster:
https://en.wikipedia.org/wiki/Ethernet#Autonegotiation
Try to remove all Advertise rates on ether1 except for 2.5G base T but enable Auto Negotiation maybe? On my RB5009 I removed everything except for 1G base T full and 2.5G base T and the negotiated rate has always reliably been 2.5Gbps.
Your speedtests are currently capped by the 1Gbps rate of ether1. The RB5009 has no problem with PPPoE @ > 2.3Gbps, even without fasttrack. Here is a test run I just did with PPPoE. CPU usage is with fasttrack but I get the same speed without fasttrack, just with higher CPU load. My WAN is limited by GPON:
