Thank you, it looks like we are closer to solving this issue.
Prior to describing what happend after applying the advices I would like to ask some more basic questions:
1. Shall I update my Config Tools?

2. Shall I call Config Tools from specific path and can I use system PATH to execute tools.exe?
What happend after applying advices:
-I deleted -SDKVersion and -application com.nxp.swtools.framework.application from arguments
-I checked again mex file with Config Tools Gui and there is only "No toolchain project detected" information in Problems tab, however when I switch the view with "Tools->Device Configuration" there is an information "ERRORS: Processor not supported" in the lower part of the window

-All function that I need are working properly - "File->Export->Pins Tools->Export HTML Report" works properly
"Update Code" recognizes that pin_mux.c file was deleted/modified in order to test generation and generates it again.
-There is no errors in c:\Users\user\.nxp\swtools.log file:
maj 14, 2020 12:40:10 PM com.nxp.swtools.framework.KExCmdLine parseCmdLine
WARNING: Program arguments were not processed: "[-showlocation]"
maj 14, 2020 12:43:41 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 14, 2020 12:43:41 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 14, 2020 1:26:32 PM com.nxp.swtools.utils.scripting.internal.ScriptApi logWarning
WARNING: Initialization code of SPI0 component in BOARD_InitPeripherals functional group is not generated due to invalid configuration.
maj 14, 2020 1:26:32 PM com.nxp.swtools.utils.scripting.internal.ScriptApi logWarning
WARNING: Initialization code of SPI0_2 component in BOARD_InitPeripherals functional group is not generated due to invalid configuration.
maj 14, 2020 1:26:43 PM com.nxp.swtools.utils.scripting.internal.ScriptApi logWarning
WARNING: Initialization code of SPI0 component in BOARD_InitPeripherals functional group is not generated due to invalid configuration.
maj 14, 2020 1:26:43 PM com.nxp.swtools.utils.scripting.internal.ScriptApi logWarning
WARNING: Initialization code of SPI0_2 component in BOARD_InitPeripherals functional group is not generated due to invalid configuration.
maj 14, 2020 2:13:24 PM com.nxp.swtools.framework.KExCmdLine parseCmdLine
WARNING: Program arguments were not processed: "[-showlocation]"
maj 14, 2020 2:14:07 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 14, 2020 2:14:07 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 14, 2020 2:14:07 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 14, 2020 2:14:07 PM com.nxp.swtools.clocks.data.model.SettingsConfig getSettingValue
WARNING: Setting value of "OSC::CR[RANGE].bitField" has not been initialized yet.
maj 18, 2020 12:27:32 PM com.nxp.swtools.framework.KExCmdLine parseCmdLine
WARNING: Program arguments were not processed: "[-showlocation]"
maj 18, 2020 12:34:37 PM com.nxp.swtools.framework.KExCmdLine parseCmdLine
WARNING: Program arguments were not processed: "[-showlocation]"
- I noticed that new entries do not appear even though the errors are repeated and deleted log file content.
- I tried once again execute command line call
C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp
λ tools.exe -noSplash -consoleLog -Load C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp\good_example.mex -HeadlessTool Pins -ExportAll C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp
- This time HTML file was generated (as well as empty csv file) in proper place, but with this error code:
Pins model not supported for the selected target Processor
- There were no new entries in log file.
- I tried calling toolsc.exe with the parameters listed below and a few other combinations but there was absolutly no console informations.
C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp
λ toolsc.exe -noSplash -consoleLog -Load C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp\good_example.mex -HeadlessTool Pins -ExportAll C:\user\workspaces\mcuxpresso_11_1_1_first\good_example_bsp
- Error level was set to 2 after calling toolsc.exe
C:\dsabala\workspaces\mcuxpresso_11_1_1_first\good_example_bsp
λ ECHO %ERRORLEVEL%
2
Best regards