In my case, using 8+ textures, painting terrain result in poor performance. Also noticed that the Brush Size is very big factor in performance. Using smaller brush size the performance is better, but adding more textures, performance drops again. Tested on 300x300 and 4k textures, same results. On more powerful machines it might take more textures to reproduce.

To reproduce:
1. Open attached project "terrainpaintlag.zip"
2. Open "level1.unity" scene
3. Select terrain game object from the hierarchy
4. Open Paint Texture tab in the inspector
5. Select the first texture
6. Try painting it on the terrain

Expected result: painting is fluent, not lagging
Actual result: painting results in bad performance

Reproduced on: 5.4.6f2 5.5.5f1 5.6.4f1 2017.1.2f1 2017.2.0f3 2017.3.0b7 2018.1.0a1

Notes: system specifications:
GPU: AMD R7 360 Driver: 17.9.1
CPU: AMD FX 8350
RAM: 16 GB