FSRM Quota in DFS - Windows Server 2012 R2
Solution 1:
FSRM quotas are independent of DFS. When using the DFS path for a replicated share, you will see the quota of ultimately whatever file share server you get routed as configured within DFS management. You can test by disabling the target where you don't have a quota set.
The way I have always managed this in the past is simply applying your quota on both share servers. You can build some automation around it using dirquota or the new PowerShell cmdlets.