Should expansion gaps in an OSB3 roof be filled before installing EPDM roofing?
Gaps between the sheets are specified by the manufacturer because the gap allows for a bit of movement - expansion, in particular - to be absorbed without causing any buckling in the roof deck. If the gaps are filled, whether with sawdust, other debris, or an intentional sealant, then their ability to absorb expansion will be compromised.

Laying an EPDM membrane directly over the panels does pose a challenge: the gaps between panels may telegraph through the membrane and this may be unsightly. Ask the membrane supplier for a recommendation. For example, they might suggest applying some kind of tape over the OSB joint gaps and possibly applying a mastic over the tape to smooth it further.