It is possible to paint tilling materials in Substance Painter by using a specific project setup.
This tutorial will show how to prepare a specific mesh and how to work in Substance Painter with it.

1 - Creating a tilling mesh

> This mesh can also be downloaded, ready to use in your project <

To make the material tile properly, it require a plane with specific UVs.
The size of the mesh doesn't matter, but its divisions are important. The mesh has to be divided in 3 sections on each axis to present a grid of 3 by 3 squares. Creating in total 9 squares.

Now each quad of the mesh has to be unwrapped to fill the whole UV 0-1 range.
In Maya for example this can be done simply by selecting all the faces and using the "Unitize" function :

The goal is to have each quad overlap each other in the UVs.

Now that the mesh is ready, export it as an FBX or an OBJ file to import it into Substance Painter.

2 - Creating a project

It is time to create the new project in Substance Painter. Start the software if it's not already the case.

Go to the File menu and choose New : 

Click on the "select" button in the new window to load the mesh :

On done, click on "OK" (you can match the settings of the screenshot or use your own) :

If the viewport seems empty, don't worry !
It's simply because the plane is perfectly perpendicular to the camera and has no height. Simply rotate the camera to make it appear : 

3 - Painting without creating seams

The project is ready. Because of the way the mesh is made, it is now possible to paint at any place of the plane and have the brush strokes be repeated, allowing to create seamless textures. This is possible thanks to the overlap of the UVs.

To ensure a seamless texture, be sure to tweak the tilling parameters of the fill layers/fill effects properly to no creak visible seams.
Do not use random rotation for example, keep 90 degrees based angles instead.