5200,
I think you answered your own question when you said " I have seen variations between our polars and actuals "  
Polars as provided by a VPP are theoretical in nature and IMHO should be considered a starting point for developing a good polar for your individual boat.  Maybe as you get everything dialed in on the calibration front you need to bring the polar up to a higher standard as you did with calibration.

You might need an additional polar  tweaked for say  'rough water' but start by developing an accurate polar for normal conditions.  Constantly update the polar until is gets closer to 'actual'.

Good Luck,
Ernie

 

This will get deep shortly, but the questions now become:
1.  All calibration being good, when do you swap from inshore (100% optimal flat water polars) to less optimal offshore polars because you aren't achieving 100%, and therefore being under on the laylines?
2.  What's the relative shape of the offshore (suboptimal) polars, noting that the input conditions under which suboptimality might occur are multivariate (waves, imperfect or light crew, poor driver or trimmers, old sails)?
I've played with suboptimal polar modelling  ...... it gets pretty complicated pretty quickly ..... and the return isn't large.  So maybe the right question is something like - at what theoretical % are you modelling your optimal polars?  If you set the bar at 100% i.e. nothing below that is considered in setting the polar curve for any TWS/TWA, then what do you do to manage the 90% of the time when you aren't achieving 100% for all the reasons that are yacht racing?  Or do you set your polar bar at 98%?  96%?