Tom,
Thanks for the update, I was not aware than MCOD was not recommended anymore...
Things are changing so fast 
I do not think it can be an issue if just used for a Java schema that does not hold that much of tables and that never undergoes heavy access. At least on Oracle I could not think of any draw back.. .
If you've got a reference I'll be glad to read it.
Kind regards
2122670 - How to split MCOD system into single SAP System.
SAP does not recommend to run SAP Netweaver based systems on SQL Server as MCOD(Multiple Components in One Database) configuration.
2146542 - DB2-z/OS: Don't use MCOD!
MCOD is generally available and there is no intention to de-support this installation feature.