I think the year ending #1 might be out of roger's hands simply because of the tournaments Roger might skip. Roger may skip Toronto, Shanghai and maybe Paris (as basel, paris and WTf are back to back whch is INSANE).
If djokovic plays Toronto, Shanghai and Paris, and Roger skips them, he'll have a shot at gaining 3000 points max over Roger.
I don't really know if the year end #1 is something Roger is really focusing on. We know he had the goal of gaining back #1 and winning slams as well as the gold medal in the olympics. My take is that if it is something he has his mind set to he'll do his best to achieve it. If not he might skip some masters and focus on Olympics, US Open, Basel and WTF.
considering how the rankings are, skipping and losing early are quite the same : the rankings reward when you go very far in the draw and especially win the tournament.
Then there's no problem at skipping one or two tournaments if anyway you would not be in good condition and above all if you do great in other tournaments. It can require skipping Shanghai for instance to be in great shape for Basel+Bercy+WTF, or it can require skipping Bercy to be great in the WTF, it all depends on your body and shape. Playing tournaments just to play them like Djokovic in Bercy last year doesn't earn you a lot rankings-wise.
Yes, as far as the rankings are concerned, it would be better to skip the Olympics and play Toronto than the opposite, and playing both might not be good for the body, but anyway none of those prevents anything.
The one who will be number 1 will be the one who wins most, the US Open being of course the most important one, but there are many important ones : the WTF and the 4 MS1000 tournaments as well, 4 ones being a lot, it will all be important tournaments to win, but anyway it's not really about taking part, it's about winning. I'm not sure the year-end-number 1 will be the winner of the US Open : there are too many other big tournaments in that period.
I'm sure he cherishes that goal to get that number 1 in the end of the year, I remember how he was happy after he defeated Murray in the WTF 2009 and was certain of the end-of-year number 1. But he doesn't have to make a choice between "do you prefer winning the US Open and not finishing the year as number 1 or the opposite ?" anyway.
Anyway, it will all be about a precise planning about how to take part but also how to be in good shape for these tournaments.