USB trace impedance calculations, with termination resistors
question 1:
This doesn't seem right 


The default Er is 4, but usually the ER for standard FR4 is around 4.6. Although for this calculation you will need the effective Er because the top of the trace is not embedded in FR4. 

with Er=4.6, conductor with=0.17mm and dielectric height of 0.08mm the effective Er is 3.2215.
but the EEWeb Edge Coupled Microstrip Impedance Calculator not giving me the same values as the polar si800 field solver or the free Saturn PCB toolkit. 


use the Saturn PCB toolkit it is free and it alco can compensate for the plating trapezoid shape of the traces and other production process variables.

question 2:
The trace impedance should be as close as possible to the caracteristic impedance of the cable, the connector and the termination on the receiver end. Any impedance discontinuities will cause reflections and cause degradation to the signal. So keep the trace differential impedance asc lose as possible to 90ohms the single ended impedance is important but not so important because in the cable the signals are transported in a differential pair. the series termination resistors are used for 4 main reasons. 


To reduce EMI this is if the product is going to be EC approved.
To absorb near end reflections like the ones caused by the connector.
To control/reduce the signal level in the receiver end because there are maximum drive voltage limits in the HS-USB compliance test.
To crudely improve ESD protection (when the system needs better ESD protection a proper low capacitance clamping device should be used instead)


The only undesired effect is increased slew-rate, but the manufacturer recommendation  usually takes this into account.

As a example of using the series resistors to improve compliance please see the following picture. Although the eye diagram perfect, the teat packet failed because it went over the boundaries as signaled by the 3 red dots in the bottom right of the template boundary box. this is because there is some overshooting. The series resistors can be used in this case to reduce the overshooting.


the test passes after increasing the series resistor value by 10 ohms.

Guidelines:


Keep the series termination resistors as close as possible to the
pads of the driving device for better absorption of the near end
reflections. 
Avoid running the running the differential pair over a
ground plane discontinuity.
Keep the differential pair away from any vias, pads or copper in the same layer at least 3 times the inter-pair skew or the dielectric height whichever is the largest.
simulate everything
if you can reuse a design that is already passing compliance, just do it don't reinvent the wheel.