Unfortunately Zillow derives much of its value information from sales that are not current. Yes, realtors do check values and run comparable market analysis prior to placing a value on a listing. There is lots of good information on Zillow but they are frequently out-dated on current values when homeowners depend on their information on pricing. Especially, since today we are in a "seller's" market. I agree with you that values have increased in the past 6 months. I hope this helps to understand the Zillow estimate.
There is an obvious discrepancy in value - oftentimes values posted through Zillow are only guidelines (not accurate value) and they may be looking at the date of purchase which is not an accurate way to do this. In order to obtain value you need to look at what similar properties have sold for in the past 6 mos in similar neighborhood. I never look at the value of the attached unit but rather consider sales in the area and what the market inventory is if you were to considering selling. One of these numbers is not accurate and without viewing the property I cannot tell you which one is incorrect. I hope this information is helpful to you.
You mention the other unit is $45K more than yours - can I assume you both have your properties listed for sale at this time? Perhaps there is a difference in the interior condition/upgrades? What street are you located on? I would need to understand how you know for sure there is a $45K difference as the recent market has been changing with values are on the rise.
Property values in Central Davis are fairly good these days - perhaps a rental would be a safe bet (depending upon the amount of rent you will charge). I agree a good tax accountant would be your best resource as this will end up a tax question when all is done.
Commission varies by areas and market competition. I always recommend you start at 6% but can reduce to 5% if there is a need to do this later in lieu of price reductions. I don't want to lose any agents who will look at commissions before determining what properties to show (I do not do this but many out-of-area agents will). My time and expensive marketing programs warrant the higher commission and my job is to get the home sold in the shortest amount of time - so whatever it takes and seller agrees is what I will do.
What property are you searching for that you cannot find?