This is true when you ship a installable binary. But if you just provide your plugins and “users” of these have to install the dependencies this makes a difference.
For our product “ABAP Development Tools” SAP has customers where the computers where your Tools are installed don’t have access to the internet (because it’s military industry for example). All these customers would have to adapt their installation procedures.
I also not a big fan of that scenario but that’s real life.
EPP packages are more or less meant to be "final" and are not to be seen as immutable, API-ish packages that you can build upon and assume they will never change for many years.
So assuming that your tools build on top of a package that will forever have XXX available is unsafe and will lead to other cases like this one in the future. If you want to guarantee Mylyn is present upon installation of ABAP Development Tools, then it's ABAP Development Tools duty to properly express it does *include* Mylyn and to be ready to ship it.
For Code Ready Studio, the p2 site does include as reference a *full copy* of the target platform; and a zipped p2 repo containing everything including target platform is shipped (it's actually the RCP product repo). As a result, if tomorrow XXX is removed from EPP, SimRel, whatever, then the installation procedure doesn't change for users of this "complete" p2 repo archive.