Pi-hole values privacy as high-value goal. We provided the patch implementing the new config option no-ident only recently to the dnsmasq project to allow removal/suppression of these strings (before this was only possible through recompilation from source).
However, the patch - submitted to dnsmasq also only affected said dnsmasq code and the extra version.ftl was forgotten to be added when importing out patch from the upstream project into ours.