I think you probably should know by now that creating a custom template with the same name as an existing one will overwrite everything from the original one. As per the documentation.
As I said in my question the file name for the custom template is ZZcustom and is intended to go in
/etc/e-smith/templates-custom/etc/php-fpm.d/ibays.conf/ZZcustom
which I purposely did to avoid conflict with 10Ibays.
What I wanted to know is will it create a problem since the resulting expanded template structure will look something like this?
[Primary]
default SME PHP settings
[other-ibays]
default SME PHP settings
[Primary]
custom max_input_vars setting
[other-ibays]
custom max_input_vars setting
I'm just wondering if having a second set of settings for each pool will add to the settings in the first set since they aren't duplicated or cause the first set to be ignored. I know in the regular php.ini if a specific setting is listed twice, the second one is the one that is effective. I don't know if this is true for pool groups for php-fpm.
I see from the link you gave that the plan for SME 11 is to split the 10Ibays file so that the end of loop is in a separate file to allow for custom template files to be put in the middle which would solve this issue instantly.