Yes, it is possible to disable the checks individually. As a matter of fact, I've already disabled modernize-use-using in my script, because it fails more often than not. My guess: my version of clang-tidy is missing this patch.
I'll run a modified script with modernize-use-auto disabled as well. Wish me luck. :D. I'll push another commit to a different branch with those changes.

Just as an added input, can you tell me which among the following look out of place so I can disable those also.
modernize-avoid-bind
modernize-deprecated-headers
modernize-loop-convert
modernize-make-shared
modernize-make-unique
modernize-pass-by-value
modernize-raw-string-literal
modernize-redundant-void-arg
modernize-replace-auto-ptr
modernize-shrink-to-fit
modernize-use-auto
modernize-use-bool-literals
modernize-use-default-member-init
modernize-use-emplace
modernize-use-equals-default
modernize-use-equals-delete
modernize-use-nullptr
modernize-use-override
modernize-use-transparent-functors
modernize-use-using