Amphibious ships do not create an army

Could Japan's amphibious assets quickly mount a Malaya- or Philippines-scale invasion?

Not by themselves: ships are only one part of an invasion, which also needs many troops, merchant transport, equipment, and time to assemble.

Specialist ships such as Shinshū Maru were impressive amphibious assets. A ship and its landing craft do not, however, create the divisions needed for a Malaya- or Philippines-scale invasion. Japan would have to withdraw troops from existing operations, concentrate them, assemble equipment, and take merchant shipping out of trade. Those transports would then need protection throughout their movement to the objective. The 1939 scenario therefore denies Japan the ready-made force package associated with its later conquests.