Perhaps NOT hopes to get the FN communities to push for acceptance of the EA, including the mine proposal, rather than raise objections, because this road will benefit them directly. If separate EAs were put forward, they might put their voices behind the road proposal, but might still oppose the mine. It is likely NOT intends to upgrade or build those parts of the road which will be used by their trucks, but will leave the branches going to the FNs to the Govt to fund and build.
The other consideration might be, there is no point in building the road unless they get permission for the mine, so it makes sense to apply for both at once.
The more southerly east-west route could be built by the Govt solely to serve those FNs in that general area, without a link to the north along the esker. A case could be made for Federal funding for this, to serve those FNs (Eebomateng, Marten Falls).
I don't know how possible or cost effective it might be to build that as a light duty allweather road initially, and later join it to the ROF (northward section) and upgrade it to a heavy duty transport road. The advantage to this route is the fewer bridges compared to following the esker all the way, and the disadvantage is the longer distance. A little shorter than the NOT route, and longer than the direct north-south esker route, I think.