<< I've heard that sometimes equipment might be configured for a manufacturer's needs, which could make it difficult to work with >>
That usually refers to OEM stuff manufactured for a particular company like Dell, Gateway, etc., not the OEM stuff you would buy from an online reseller. (or local mom&pop shop) For the most part, the OEM stuff you'd buy from Newegg, etc., is the same as retail except you don't get certain things. No fancy box. (who cares) No fancy manual in some, but not all, cases. As far as drives go, you usually do not get a cable with them. (big deal) You usually get whatever software/drivers are appropriate for the item. (even tho there is usually more recent stuff at the manufacturers website)
Stuff labeled as 'white box' is usually identical to retail except it will come in a plain box.
Depending on the item, warranty could be different. Drives have the same warranty as their retail flavors. CPU's on the otherhand are only warrantied by the reseller - you have to go to them for replacement if you have a problem and the length of warranty varies between resellers. All depends on the item.