Let's back up and consider that a rain screen is normally recommended in a very high rainfall zone and if I'm not mistaken, that is not the case here. So, if a lot of water is not expected to enter the cavity, I would skip the back priming and treat this installation as vertical cedar boards on horizontal furring assuming the projection of the window frame is large enough to allow 3/8 furring strips and the addition of a sub-sill will restore the missing drip. Hopefully the ends of the boards would either be free to drip or under flashing and would not need to be primed or sealed. Of course, I say this without knowing anything about the design of the house...what my old boss would call designing in a vacuum. The final design of the siding installation will be largely determined by that information rather than general advice.

For vented siding to have any effect, air must be able to move between the wall and the siding. With horizontal furring and vertical siding, how will you get air flow? As far as your specific question, if the top of the siding vents into the soffits and the soffits are vented and screened for bugs, no further screening is necessary. But, again, if your furring is horizontal, what allowances are being made to keep air moving behind the siding?

Although cedar looks nice, it can create a host of issues depending on the area. Lived in a cedar roof house where the cedar attracted flying squirrels, which can chew through anything and they did, landing themselves a home in our attic. Repaired their damage and replaced with asphalt shingle, and problem disappeared along with the cedar. I'd take woodpeckers over flying squirrels, but would rather have neither and accept a "cedar look". Everyone is assuming the builder is changing things on specifications, which could be the case, but could also be the case of the OP reading into the renderings too much. Spec homes are generally not "one off" homes and the plans may be used again, tweaked, etc., by the builder and builder's architect. So, renderings are "artist design" only and not always representative of exact finishes. Rarely does a builder pay for renderings to represent every possible finish on a house and if he/she did, would have to increase house price to reflect "eye candy drawings". The specs going in the house are determined more by what pencils out for that home site, location, build costs, demand, etc. Maybe 9/10 people looking at possibly buying this home want hardie and the builder knows that, hence cedar wasn't in the design specs to begin with or builder realized this and changed. Either way, when looking to purchase a spec home, go by the specifications, spec sheet, start pack, whatever the builder calls it, to determine what is going in the home (not a rendering). BTW, this also goes for the landscape in a rendering. Don't assume that 100 year old hardwoods will be brought in for your project just because they are shown in a rendering (it would be funny if wasn't so close to true).

Find the manufacturer's installation directions for whatever the replacement window will be. Here's Andersen's: https://images.homedepot-static.com/catalog/pdfImages/27/273888e4-efab-4463-a51f-20b85cb44957.pdf best way to get water tight seal?? Remove the siding so the window can be properly flashed. $1400 more now but a fraction of what it will cost to replace it (again) later. When this rotted window comes out, be sure you're there to see it and get the forensics of why the installation failed. I'm betting that knowing that will make you feel a lot better about the addt'l expense for removing some siding. Oh, and the upside is that you have cedar so trying to match new siding to old siding shouldn't be a problem.