Motivation 1 ('organisms-as-agents thesis') "says that organisms really do exhibit some or even all of the attributes of agency". Motivation 2 ('organism-as-agents heuristic') "says that it can be heuristically useful to treat organisms as if they were agents for certain intellectual purposes".
It's interesting that both motivations appear to be about modelling organisms as agents, as opposed to any other level of organisation. This feels like it misses some of the most interesting insights we might get from biological agency, namely those around agents at different levels of organisation interacting - e.g: ants and ant colonies, cancer cells and multicellular organisms, or individual organisms and selection pressures (which could be treated as as-if agents at evolutionary timescales).
1Okasha's paper is addressing emerging discussions in biology that are talking about organisms-as-agents in particular, otherwise being called the Return of the Organism turn in philosophy of biology.
In the paper, he adds "Various concepts have been offered as ways of fleshing out this idea of organismic autonomy, including goal-directedness, functional organization, emergence, self-maintenance, and individuality. Agency is another possible candidate for the job."
This seems like a reasonable stance so far as I can tell, since organisms seem to have some structural integrity -- in what can make delineated cartesian boundaries well-defined.
For collectives, a similar discussion may surface additional upsides and downsides to agency concepts, that may not apply at organism levels.