You don't technically have to disclose internal mods to all employees because everyone is part of a single legal entity and no binary distribution occurs.
Perhaps but then you will kick yourself the first time you want to give a customer or business partner access to your modifications. Unforeseen business needs or opportunities can always make you need to distribute a tool you previously thought would only be internal. I'm not saying this is a slam-dunk reason to not use GPL tools, but I'm just pointing out that there is a legitimate worry here that is not fully alleviated by your point.