Sorry for not posting back sooner (too far from civilisation when at home for internet!) but after some poking around in my Wacom’s settings I found why I hadn’t experienced your problems.
Although AR5 is a separate App I have all the physical buttons the same as in AR4. So never noticed what was actually happening. But I have set different on-screen buttons for AR5 successfully. I think these virtual buttons though are not tied directly to specific apps and could be called up by any app if you wanted.

It seem that my AR5 is using AR4.5’s Wacom settings. Set what you want there and it works fine in AR5.
I tried deleting and re-setting AR5 as a separate App but the tablet refuses to recognise it as such. And indeed if I delete the AR4.5 tablet preferences I’m left with no tablet support in AR5.
I’m not sure if this is an AR bug or a Wacom bug?

As for the Pen Eraser I couldn’t assign the Colour Sampler tool to it directly but I could set it to emulate the alt/Option key, which will let you sample colours using whatever settings that the Colour Sample tool is currently using.