InputCommon: fix InputConfig::LoadConfig() not always replacing emu controllers values

If InputConfig::LoadConfig() was called once with a non empty/customized config,
then called again after manually deleting the config (dolphin calls LoadConfig() every time it opens the mapping widget),
the second load would fail to clear the values on any non first EmulatedController and would instead keep the
previous config values despite it being deleted (while it would instead correctly default the first EmulatedController).

This is not a big bug though the code is better now.

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