Adopt and Skin-beta.1.7 is out! This adds a fix for pet placement on custom farm maps.
It has three new config options: Enable custom placement, placement X position, and placement Y position. It'll need to be enabled or the X and Y won't do anything and will use map default. If you're having trouble getting your pets to spawn in an accessible spot on a custom map, edit the config to enable custom placement and find the X and Y of the pet bowl or wherever you would like them to spawn on the map. (You can do this using the Debug Mode mod, or by opening the map in Tiled and hovering over the coordinates.)