Is it required to physically separate Part-21 stock from Part-145 stock?
No, there are no formal requirements in the EASA Part-21 or -145 regulations requiring physical separation of Part-21 stock items from Part-145 stock items.
What is important, is that the Part-145 may only use parts listed in the IPC/IPL. Part-21 can use items for proto types or from drawings. These parts should not be issued in a Part-145 environment.
The parts or items in the shared stockrooms must of course be provided with batch numbers, locations, etc. The entire trace and end-use (Part-21 and/or Part-145) must be recorded in the ERP.