For anyone interested, setting the partition type correctly actually did the trick. Haikuloader now correctly boots without having to manually choose the partition.
I took the partition GUID from haiku/gpt_known_guids.h at 8f16317a5b6db5c672f331814273e5857555020f · haiku/haiku · GitHub and used DISKPART on windows to set the partition type id ( select partition X and then set id=X ).
The GUID is formatted slightly differently in Haiku codebase as it’s divided in 4 chunks, while diskpart wants it in 5 chunks, but it’s as easy as adding the extra dash ( 42465331-3BA3-10F1-802A-4861696B7521 )