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IDK why it dislikes the MakeCert files. Clearly a bug, to me.
This is basically by-design, but the design could certainly be improved. The basic idea is that, if you install a certificate generation extension (e.g. the BCMakeCert extension), it will be used.
If you do not, then Fiddler will fall back to using the built-in generator, which itself has two underlying engines (MakeCert.exe or CertEnroll.dll).
FWIW, the BCMakeCert extension should be slightly superior to the built in CertEnroll provider (it has more features and touches the Windows certificate stores a bit less) although they're pretty comparable.
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