Autoanswer...
Yes, this is possible. As @Wosi suggested you can write a batch and then call it with $f parameter added.
Sample batch (signtool.bat):
@echo off
"PATH_TO_SIGNTOOL\signtool.exe" sign /v /du "COMPANY_NAME" /fd sha1 /t "http://timestamp.verisign.com/scripts/timstamp.dll" /f "sha1_cert.pfx" /p PASSWORD %1
set SIGN_RESULT_1=%ERRORLEVEL%
"PATH_TO_SIGNTOOL\signtool.exe" sign /as /v /du "COMPANY_NAME" /fd sha256 /tr "http://timestamp.comodoca.com/rfc3161" /td sha256 /f "sha256_cert.pfx" /p PASSWORD %1
set SIGN_RESULT_2=%ERRORLEVEL%
set /a RESULT=%SIGN_RESULT_1%+%SIGN_RESULT_2%
if %RESULT% NEQ 0 (
echo Warning! Signing failed with %SIGN_RESULT_1% for sh1 and %SIGN_RESULT_2% for sha256
pause
exit /B %RESULT%
)
echo Signing succeeded
exit /B 0
Then in Inno Setup you can call signtool.bat $f where $f will be passed to %1 for the batch.
For Windows XP compatibility for sha1: removed /as, /tr replaced with /t, removed /td (as it requires /tr)
I will leave it here as maybe someone could find it helpful.