I think that is because the database of possible fares between East Croydon and Whitechapel does not have a “via Farringdon” option (or is it because the touch on the validator is disregarded, and the outcome would have been different had the passenger done an out-of-station interchange at Farringdon instead?). The default fare is zones 2-5. In order to be charged a zones 1-5 fare on this journey, you would need to do an out-of-station interchange at one of the stations defined on one of the three alternative routes. At present, Farringdon is not included as a possible interchange station in the definition of any of these zones 1-5 routes, hence you are charged zones 2-5 notwithstanding your touching on the validator at Farringdon (which is unnecessary, by the way, unless you were switching between a paper ticket and pay-as-you-go).
More broadly, there are a lot of journeys for which the default and alternative routes do not take the Elizabeth line into account. For example, Stratford to Abbey Wood has two defined routes, the default being zones 3-4 (I imagine the idea would be to go via Canning Town and Woolwich Arsenal), and the alternative being zones 1-4 (“Via Zone 1 changing between London Underground and National Rail at Blackfriars, Cannon Street, Charing Cross, London Bridge or Waterloo East (or Victoria or Waterloo”). An obvious route, taking the Elizabeth line to Whitechapel then doing a cross-platform interchange to get another Elizabeth line train to Abbey Wood is not defined (it would have been zones 2-4). Of course, given the lack of any out-of-station interchange, it would be impractical to distinguish between “via Canning Town and Woolwich Arsenal” (and thus zones 3-4) and “via Whitechapel” (and thus zones 2-4), so I suppose it is right and proper to make a presumption in the customer’s favour… unless TfL want to institute pink card readers at Canning Town and/or Woolwich Arsenal and require customers to use them for a “not via zone 2” fare (does such functionality even exist? As far as I am aware, pink card readers are used only to indicate “not via zone 1” fares for journeys where the default route is via zone 1).