+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.
Best Answer
Typically what you're asking for is achieved by using a Reverse Proxy in front of the sites. Some popular dedicated options include HAProxy and NGINX.
It also appears that IIS by itself can potentially do it with the URL Rewrite module. Here's a blog post with more info: