It is true PMTUD is for TCP packets but also for some tunnel protocols such as IPSec, GRE etc. PMTUD is defined in RFC 1191.
It is important to remember what PMTUD is for, it's purpose is to measure the smallest MTU on the path and then the originator will then send datagrams smaller. PMTUD is a very important way of avoiding fragmentation and as we all know fragmentation can be the cause of increased packet loss rate and increased CPU.
Now to answer how does IPSec and PMTUD work together?
IPSec encapulation will copy the DF bit to the external header, then IPSec will keep track of the path MTU of the tunnel.
Some further information is all available on CCO, but here is one good reference:
Table of ContentsIntroductionVersion HistoryPossible Future
UpdatesDocuments PurposeNAT Operation in ASA 8.3+ SectionsRule Types
Network Object NATTwice NAT / Manual NATRule Types used per SectionNAT
Types used with Twice NAT / Manual NAT and Network Obje...
Table of Contents Introduction:This document describes details on how
NAT-T works. Background: ESP encrypts all critical information,
encapsulating the entire inner TCP/UDP datagram within an ESP header.
ESP is an IP protocol in the same sense that TCP an...