When changing layer with tile pattern active, the pattern gets messed up

[KoBeWi]

Godot version

c2a616f

System information

W10

Issue description

The blue and red icon are in different tile atlases.

Steps to reproduce

1. Draw some tiles using multiple atlases as sources
2. Use Picker tool to select a pattern
3. Change layer

Minimal reproduction project

AtlasPatternMess.tscn.txt

EDIT:
This actually happens even if the tiles are from the same atlas:

[KoBeWi]

Reopening. The issue is back in 4.3 dev6, likely after TileMapLayer changes.
CC @groud