It was our intention to allow the button to be positioned anywhere, this sounds like a bug. I agree, we'd like the flexibility to do what you are trying to do.
It might be possible to hack in some CSS to gain more control of the _playButtonRootElement div element or use the #excalibur-play id to manipulate the button element. Another workaround may be to return an position absolute/fixed button out of the loader.startButtonFactory() and position manually.
Please open an issue in github
https://github.com/excaliburjs/Excalibur and describe exactly what you're trying to do with the play button. Please let us know what values you think would be valuable to pass to the loader to customize button position.
I'll have some time to look at this bug on Saturday, sorry about the hassle.