The patent agreement part GPLv3 (which is the difference between GPLv2 and GPLv3 in regard to patents), only cover distribution rights. If you do not distribute the whole work, you can create as many code contributions you want and have as many patent license agreement at the same time. They do not interact.
For code contributions, GPLv2, GPLv3 and Apache license has the exact same deal in regard to patent grants. Actually, the text used in GPLv3 that cover patent grants of contributors, is word for word copied out of the Apache license. GPLv3 only added additional patent requirements for distribution of the complete work. My guess, for the exact reason of not discouraging companies to contribute code.
If the company review GPLv3 contributions, but do not review Apache licensed contributions, they have bitten the FUD apple.
For code contributions, GPLv2, GPLv3 and Apache license has the exact same deal in regard to patent grants. Actually, the text used in GPLv3 that cover patent grants of contributors, is word for word copied out of the Apache license. GPLv3 only added additional patent requirements for distribution of the complete work. My guess, for the exact reason of not discouraging companies to contribute code.
If the company review GPLv3 contributions, but do not review Apache licensed contributions, they have bitten the FUD apple.