+1 for @ahmelsayed his answer. But you can create multiple FastCGI applications in IIS, with different php.ini files easily with Appcmd. But only one handler/php.ini per application pool, see:
Set up two FastCGI applications:
Appcmd.exe set config /section:system.webServer/fastCGI
/+"[fullPath='c:\php5\php-cgi.exe', arguments='-c c:\php5\php.site1.ini'],
maxInstances='0', idleTimeout='300', activityTimeout='70',
requestTimeout='90', instanceMaxRequests='9999',
protocol='NamedPipe', flushNamedPipe='False']" /commit:apphost
Appcmd.exe set config /section:system.webServer/fastCGI
/+"[fullPath='c:\php5\php-cgi.exe', arguments='-c c:\php5\php.site2.ini',
maxInstances='0', idleTimeout='300', activityTimeout='70',
requestTimeout='90', instanceMaxRequests='9999',
protocol='NamedPipe', flushNamedPipe='False']" /commit:apphost
Each web site then can have its own Handler for .php, pointing to one of the php.ini files:
AppCmd.exe set config "site1.com" /section:system.webServer/handlers
"-+[name=`'PHP`',
path=`'*.php`',
verb=`'*`',
modules=`'FastCgiModule`',
scriptProcessor=`'c:\php5\php-cgi.exe|-c c:\php5\php.site1.ini`',
resourceType=`'File`',
allowPathInfo=`'true`',
requireAccess=`'Script`']"
AppCmd.exe set config "site2.com" /section:system.webServer/handlers
"-+[name=`'PHP`',
path=`'*.php`',
verb=`'*`',
modules=`'FastCgiModule`',
scriptProcessor=`'c:\php5\php-cgi.exe|-c c:\php5\php.site2.ini`',
resourceType=`'File`',
allowPathInfo=`'true`',
requireAccess=`'Script`']"
If you don't like the command line, you can click your way through IIS Manager of course :) BTW, assuming correct configured application pool identities and NTFS file permissions, I believe there is no need for open_basedir.
Edit: Two references: https://www.saotn.org/php-wincache-on-iis/ and https://www.saotn.org/custom-php-version-iis-express-webmatrix3/ to show how to add multiple FastCGI + PHP applications in IIS.