Pay now, query later

I am fairly new in practice and haven't yet had this situation but wonder how I should advise a client if and when it arises.

That is, HMRC apparently adopt a stance of "pay now, query later", which can be expensive and difficult for clients where there is a query involved. The example someone cited to me was re incorrect PAYE coding where HMRC said they should pay what was due and query it later, in order to avoid further penalties / interest. 3% is a fair cost compared to most savings rates currently available - but is it harder to get money back once paid to HMRC if it's agreed it should not have been due after all? Should I advise my cleints to do as HMRC say and pay now, query later, or should they hold off and if so, presumably risk interest if not penalties. I'd like to understand how others deal with this.