yes. this is intentional for a couple of reasons First, keep in mind:
* two-finger tap is easier to trigger than a three finger tap
* two-finger tapping is reliable on virtually all touchpads, three-finger tapping is an issue on many older touchpads

Now, with that in mind. 
* In most UIs right click is more important than middle click and should be easier to trigger.
* in most UIs, right click is non-optional - some menu options are only accessible via right click so having a working right click is imperative. I think only OS X is the exception here.
* in most UIs, middle click is a hidden feature. Yes, it does things like paste or 'open URL', but these are not obvious or even mandatory

So these arguments go in favour of the current setting.
There is other precedence: the average mouse has a dedicated right click button but middle click is on the scroll wheel and harder to trigger.


So the main question is: what is your workflow that you need to change this around and you can't use three-finger tap to middle click?

ok, that'll teach me answering bugs before the coffee kicks in. See my comment, we hardcode finger assignment for 1/2/3 fingers as L/R/M tap. If your touchpad has an LMR that's usually caused by the touchpad not being recognised by the kernel and tapping is handled in the touchpad's firmware. I'll need the evemu-describe of your touchpad device please.

Oh, I'm sorry, that's a mistake, 1/2/3 fingers does corresponds to L/R/M.

I agree the hardcoded setting makes sense for most people. But there're people like me, who mess up 90% of times trying to use three finger taps (it always ended up being a two finger tap), and use middle click more often than right click (copy-paste, open in new tab, etc.).

Making it configurable won't harm, right?

(In reply to Yuxuan Shui from comment #3)
> Making it configurable won't harm, right?

it's a fair amount of work to add any configuration option because we now need a testing matrix for each combination. That's effectively indefinitely too, users are angry to not have a feature but get even angrier when a feature is removed.
http://who-t.blogspot.com.au/2016/04/why-libinput-doesnt-have-lot-of-config.html

https://lists.freedesktop.org/archives/wayland-devel/2016-July/030208.html

Thanks a lot for implementing this !!

commit 59fac8e90269af863231752dc5897f11146f6e05
Author: Peter Hutterer <peter.hutterer@who-t.net>
Date:   Thu Jul 21 11:46:05 2016 +1000

    Add configurable button map to tappings