Hi @Beggar,
Firstly, what user manual are you reffering to? I believe the User Guide for MCUXpresso Config Tools (Desktop) contains quite a bit of useful information about identifiers, including how to disable the warnings for "Not Specified" identifiers. As seen on 'Table 10. Preferences', option "Require Identifier for Pins (Pins Tool)" enables or disables the generation of warnings for pins with no related identifier:

That said, identifiers can be very useful, specially when it comes to code congruency for the generated pin_mux files. As you can see on the following image, the identifier is only used as an 'alias' for the configuration structure used to initialized the pin on pin_mux.c (in this case, it only replaced gpio4_pinB1_config with SEMC_A6_config for congruency with the identifier "SEMC_A6"):

However, on pin_mux.h, the change between no identifier and "SEMC_A6" is greater, since a whole set of macro definitions is generated according to the identifier (which before were inexistent before the identifier was defined):

These macros are meant to be referenced during development of the application code to ensure congruency and standardize a naming convention for everything relating each defined pin. Defining multiple identifiers for each pin is also possible, but note that only one identifier can be used at once. This feature is basically only used to redefine all of the according macros at once (for example, changing "SEMC_A6" to "ID_TEST"):

For more information regarding identifiers on ConfigTools, refer to section 3.3.4.2 Labels and identifiers on the aforementioned document.
BR,
Edwin.