Is there a way to tell the CREATE editor's compiler to create an intermediate file (file set) containing the assembly sources so that I would be able to check the exact timing of my code?
In my specific case I would like to know that how much time does it take in my interrupt handler to reach a point where it changes a PIN state (interfacing an old 8bit computer)
No, there is no way to tell the Arduino Web Editor's build system to do this. The best you could do is to do an upload to get the compiled binary downloaded to your computer, then do a disassembly on the binary. If you enable Preferences > Console: Show verbose output, do an upload, then check the upload command in the black console window at the bottom of the Arduino Web Editor window, you'll see the path of the temporary folder that contains the binary file.
I don't know much about this subject, but I'm pretty sure the disassembly you get by doing this will be inferior in terms of readability to the one you would get if you use objdump to disassemble the .elf file that is accessible after you compile a sketch locally on your computer with the Arduino IDE, etc. You can use the --source --line-numbers flags to annotate the listing with the code, which I (knowing absolutely nothing about assembly) find to be essential to being able to make any sense of the disassembly listing, and this will require the code files to be available from the paths they were at when the sketch was compiled.
If you don't need the full Arduino IDE GUI for compiling locally, you might prefer Arduino CLI:
https://arduino.github.io/arduino-cli/latest/
Thanks a lot for your reply!
I was afraid if this kind of answer but I'm not afraid to use the Arduino IDE (as I was using it for years). Ok, then let's make our hands dirty (and use the IDE locally)... 
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