Hey there, sorry for late reply.
I just wanted to comment that I have exactly the same configuration, MikroTik hex S + Zyxel PMG3000-D20B, and I have an full advertised speed 300/100 Mbps, ISP A1 Croatia.
Meanwhile while surfing I came accross a post on one forum (Italian) that describes upload cap problems on Zyxel ONT’s, and problem seems to be a firmware issue on Zyxel ONT’s, and OP describe a firmware downgrade procedure:
https://forum.fibra.click/d/36541-rollback-sfp-zyxel-con-il-w3-hub-per-risolvere-il-problema-dellupload-cappato