I am in process of building my own new home. It is a 1 floor structure. I installed 2000 sq ft of white oak in alternating widths of 3", 4" and 5". The T & G lumber I used was cut 3 years ago, air dried for 3 months and then kiln dried to 7%. After that I dry stacked it in the home under construction and it remained there for 2 years with the inside temps maintained at 60 F. At that point I installed it over my sub floor of advantech and a paper barrier. I was careful to maintain a very tight installation with appropriate edge wall expansion gaps. I used staples and probably for sure way over-nailed it (anal on my own home!). At that point I did not finish or sand. I continued to work on the house for another 10 months whic brings me to today. Here is the situation I need advice on;
The floor now has plenty of gaps between boards. They just appeared in the past 3 months. I am now planning to sand and finish. My thought was after a 36 grit pass I would do a Full trowel fill and then finish the sanding steps and finally stain or just poly. However logic (or in experience) tells me that if I full fill and the season changes and the floors boards expand and close the gaps-wouldnt that squeeze the filler out? And consequently if I don't full fill and just sand and finish with the current gaps....wouldn't that look like a poorly done job? And once again what would happen to the poly once the floor expanded in the summer months? I have talked to several installers and received opinions in every direction. So since this is my own dream home and the last one in my life....I sure want to do it the best way possible.
I live in Nashville, The house has a basement. The basement ceiling is insulated

Well, you have it mostly right. The winter will be dryer than the Summer months so the wood will shrink without a humidifier attached to your house heating system during the winter as possible. Oak is a relatively stable product as far as expansion and contraction because of changes in conditions. When you sand the floors now, there will be gaps that may be filled with wood patch that will disappear, but be compressed during the humid season of the Summer. I would be sure to fill bigger gaps and let narrow gaps alone. I don't believe in trowel filling in most cases.
Gaps will tend to even out across the floor and the filler should not affect adjacent rows in the Summer since you installed the flooring after it acclimated to a different more damp season. The installation where you fastened the floor very well will keep the boards from moving when they are walked on so the filler will not pop out as easily, compared to minimum fasteners. The finish should be applied at the minimum rate that is suggested on the can, which is 400 square feet per gallon. I wait to fill the floor after sanding with at least 50 grit and sometimes 80 grit so it takes less filler as the surface is smooth.