The Benefactor is..

I suspect asset reuse but it would also allow to take the story to an interesting direction IF they ever made a sequel.

3) the Benefactor specifically offers to help with making SAM a reality when Ryder can't continue on his own anymore. Who is the org that would be developing EDI around that time?

Timeline does not fit. SAM was in dev in the 2170s. EDI was created using Reaper tech in 2184-85. SAM was completed and even further modified well before EDI's creation as The Andromeda Arcs launched in 2185.

Andromeda is not what it seems. It takes place in the past, present and future all at the same time because it's a construct build to navigate a collective consciousness. The navigator is an AI called SAM. We are not 'IN' Andromeda, we are in a simulation that takes us a billion years into the past to show us the Origins of the Reapers. Remnant + Kett = Reapers. It's that simple... Archon; 'Await my Arrival' 'It will be like you never existed' (to Ryder during Final Battle) look at the clues all over the place; Manta in the sky Hab7 & Havarl = Kett Exulted leviathan (the prodigy of the kett who were betrayed by the AI - but after the Archon corrupted the Remnant), the speeding of the cycles thanks to rem tech allowing the creation of multiple species within 50K years; You (humans) are an anomaly, but that is not enough; humans were not created by reaperized remtech - all backwards leg species were. Asari were create using humans transplanted onto Thessia and cultured by the previous cycle; and perhaps a Prothean offshoot that managed to survive, but doubtful. Think about 'Prothean' It was a name given a nameless species by humans (Revelations). Why does Javik accept that name instead of correcting the current cycle? Because you are already in a simulation in the OT. Reapers are cunning; the previous cycle was not Prothean. The protheans were the freakin Kett. Listen to Javik's description of their empire; you BECAME Prothean OR a slave race. All species follow the path planted by the Reapers (Havarl - 'Unearthed' collectable mission), the previous cycle is exactly who the Reapers want you to think they were.