mbedtls config: fix too early check_config.h includes

check_config.h was included manually by custom configuration files.
This caused compilation errors when updating MbedTLS to 3.6.0
because check_config.h was processed too early, before the whole
configuration is defined, effectively causing configuration check errors.

MbedTLS already takes care of including check_config.h at the right time.
Remove those erroneous manual check_config.h includes.

Signed-off-by: Tomi Fontanilles <tomi.fontanilles@nordicsemi.no>