A way to let clients customise AE projects

That's exactly where Plainly Videos can help. The main benefit is that your clients don't need After Effects, they can do everything just using a Web browser. You also don't need to setup any rendering infrastructure, it's all provided to you out of the box. You have the full control on what elements (images, text, media, colors) can be changed by a client and you can select various methods on how is the rendering invoked (forms, sheets, excel, etc).

They can setup a machine with AE + Templater extension from Dataclay, and use it's "Bot" mode to act as a server connected to a data source.

Templater Bot, running inside AE, will watch for new incoming data from whatever application is submitting data to it.  So, you can setup a simple form from a form builder like Google Forms, and then have those submissions sent to a Google Sheet.  Templater Bot can watch a Google Sheet — but it's more powerful than that.

You can watch this video on Adobe's Creative Cloud channel for a demonstration of the whole process.

The question is: how do the clients want to customize? If they want to customize them in Premiere Pro, you can turn your Ae project into a Motion Graphics Template, for example.