Hi Edward,
Pete has it right as the function currently works - there are no options to change the base cost for markup, using the Update Price List function. Why is it like this? For legacy reasons, and it doesn't have to stay like this for the future, but we don't typically hear too much about this function from users and thus have to assume that either not many people use it, or it works for them as it is.
Pete's suggestion is the best way to approach this, either from the Export template he suggested, or from a GridView view with all the calculations already done (from the existing Markup value stored on each item). GridView supports automatically exporting the view to Excel unattended as part of a scheduled task, so that could assist in making the process more automated.
We hope that using and supporting Adagio doesn't feel like a gamble for you.
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Regards,
Softrak Tech Support