CIVICRM_SMARTY_AUTOLOAD_PATH lets you use the newer, preferred version of Smarty. CIVICRM_EXCLUDE_DIRS_PATTERN and CIVICRM_TEMPLATE_COMPILE_CHECK both improve performance on live sites.
These are fairly new settings and your system will run ok without them. The system checks should include links to documentation telling you how to update your civicrm.settings.php file.
It's not clear to me from your question whether you actually have those values set or not. If not, then just follow the documentation and add them. If they are set and the System Status check is giving wrong results then we need to know more about your chroot setup.
==Update==
The ISP's response describes the purpose of chroot (standard stuff), but not how it is implemented, particularly as regards the webserver.
If you look at the checks CIVICRM_EXCLUDE_DIRS_PATTERN CIVICRM_TEMPLATE_COMPILE_CHECK CIVICRM_SMARTY_AUTOLOAD_PATH the code does not directly look for civicrm.settings.php but checks for PHP constants that should have been set earlier. I'm not sure how chroot would affect that.
You may need to put in some additional logging to figure out what is going on. You could start by editing one of those checks and adding something like
\Civi::log()->debug(print_r(get_defined_constants(), true)); to see what constants it does have at that point. (Don't post the output - it includes security info.)