I can think of a couple ways to do this, but neither one uses the Compliance manager. The problem is that at least currently, the compliance manager only uses the configurations that NCM downloads for compliance checking. There is no way to use another value that NPM or NCM downloads through another means to do a compliance check. So, since the "config-register" value is not in the running or startup config, you can't use this to check.
So, how can you do it? The first way I can think of is via the regular reporting engine and UnDP's. If you look, the config register is probably stored on many Cisco devices in the OID 1.3.6.1.4.1.9.3.6.9, which is the "configRegister" MIB in SNMP. So, if you wrote a UnDP to download the config-register for everything and then ran a report looking for the Cisco switches that don't have the value you want, you should be able to do it. You might have to do some decimal/hex conversions here, but that shouldn't be hard. ie: 0x2102 = 8450. One potential problem is that this OID is deprecated, so no guarantee of support on newer platforms. Another caveat or suggestion is that you might also want to look at "configRegNext" too, which is the next config register value that will be enacted once the device reboots.
The second way, which might be a bit quicker and possibly easier (depending on your techie level) is go into "Configs / Configuration Management" and do an "Execute Script" on the devices you want to check. In the script I would use the following command:
show version | i Configuration register
This will return only the line that tells you the configuration register value on the devices. From there, you can either go into each one of the show script results in the "Transfer Queue" page, or have some fun with SWQL or SQL. Let's do SWQL, although the SQL is quite similar. The results of your commands are in the "NCM.TransferResults" table, put the query below into SWQL studio and it will give you the output you're looking for in a spreadsheet format you can export. Alternatively you could add this to any NPM page, I'd suggest doing it to a new one, and just paste it into a "Custom Query" resource. Not as easy to put in a spreadsheet that way.
SELECT NT.NodeProperties.Nodes.IPAddress, NT.NodeProperties.Nodes.SysName, NT.NodeProperties.Nodes.MachineType, NT.DeviceOutput, NT.ErrorMessage
FROM NCM.TransferResults NT
WHERE (RequestedScript LIKE 'show version%')