This is where tearing out those 999 flowers by the roots comes in. Once your engineering org gets to be a certain size the benefits you can obtain by investing in making all your engineers slightly more productive start to swamp the slight gains that one team might get from doing things their own, slightly different way. During the "let a thousand flowers bloom" phase people will have planted all kinds of exotic blossoms, some of which are lovely and even well adapted to their local micro-climate; you need to be able to decide which ones are going to be first class, nurtured members of your garden and which ones are weeds.
Microsoft is definitely working through this process right now as teams standardize development atop the tools we sell, such as Visual Studio Online.