I was just working on this with another forum member after 6.39 dropped. We found that MSS clamping does in fact work. You may want to verify the MTU and MRU settings within the PPP connection. This can be found in various places depending on what is using the PPP encapsulation. In the post I will like below you'll see it in the L2TP server settings. You will also need change-tcp-mss set to yes in the appropriate PPP profile.
We'll want to make sure your MTU and MRU values are set appropriately despite any behavior of TCP MSS. Without a proper base MTU by clamping the MSS you likely aren't helping in anyway and if you are it is only helping TCP connections not ICMP or UDP.
This post we discussed the change and why the new method reserves an additional 6 bytes more than what would normally be expected under default settings: viewtopic.php?f=2&t=121457
This post you will see in the last section I dove deeper into MTU and MSS and how those settings affect the connections that traverse a link: viewtopic.php?f=2&t=121318#p596676
As a bonus take a look at the post linked at the bottom of this one. It includes some screenshots of demonstrating how encapsulation affects MTU.
You may ignore most of this post with the exception of my confirmation that 6.39 will adjust MTU and MSS of connections appropriately with default settings if you know all there is to know about MTU and MSS.