It seems that Recurrent Complex 'overgenerates' sometimes over the waystones. In most of the cases I get a village with waystone being destroyed by some building.

Update: It seems to be random. Sometimes RC is faster, sometimes Waystones - as on the screenshot below.

Is it possible to add an option to generate the waystones just outside of village border?

This might be fixed in the just released version, as a bunch of other village-generation-related issues were taken care of. If there's still issues, please reopen.

I'm not sure why that would happen, the bounding box for the Waystone structure is set correctly. Maybe the Recurrent Complex one left out that balcony? I'm not too familiar with world gen to begin with, I think you'll have more luck at the Recurrent Complex dev since they specialize with it and will probably know what's going on.