Painting Prefabs
Instantiated Prefabs are always parented to the selected Tilemap and set to the same layer.
You can use transform modification shortcuts like ALT+V, ALT+R/T/X/C/Z when previewing Prefabs. This does not affect the Prefab asset at all: when you release the mouse button, a copy of it is instantiated, has its transform modified (if only to set the position) and then painted. If you need to affect the Z-position of a Prefab prior to painting it, use the Custom Modifiers from the Painter Modifiers editor window.
It’s important to note that the preview you see when painting a prefab is an “asset preview,” like the preview seen in an inspector. It’s entirely possible and fairly easy to use the various shortcuts to create a transform that’ll place the prefab at a position and/or rotation that’d be invisible when the Scene view is in 2D mode. If it appears that your prefab disappears when you paint it, that’s probably what happened.
If the preview cannot be obtained, a ‘?’ or ‘X’ icon is displayed.
Painting Prefabs from a Bundle
When previewing a Bundle (including previewing a TileFab, which is just a collection of Bundles) up to 128 prefabs can be previewed in total, per preview cycle (which happens several times per second depending on how fast you move the mouse). So, if you have a TileFab with several Bundles and the total number of Prefabs in all the Bundles is greater than 128 then some of the bundled Prefabs won’t preview.
Aside from that, you can preview and paint Bundles (when the Bundle Tiles View option is unchecked) and TileFabs with embedded Prefabs. The preview works the same as described above: they’re asset previews. The only difference is that transform modifications are inoperative on groups of prefabs, Bundles, and TileFabs.
One advantage of using Bundles for prefabs is that any transform changes such as rotation and scale are preserved and then restored when the Bundle’s prefabs are painted via Painter or calls to the TileFabLib library.
Transform changes don’t show in the preview, and the positioning during preview may be slightly incorrect due to integer math issues.