Our current Portal system is configured to open up HCM (in a new window) by way of a link on the Portal home page. The URI for the HCM node points to the HCM system.
We have a new project underway, that will point HCM URI to a IIS site on Portal, and in turn re-direct back to HCM. However with this configuration when you click on the HCM link on the Portal page, HCM opens up with Portal boarder (the URL in the address bar would have Portal and the HCM site.
However a note that if you click F5 on that page, it reloads and displays HCM without the Portal boarders (HCM URL on the address bar). This is the desired 'look and feel'. To note, there are some instances where HCM will open fine without the portal boarder, so not 100% consistent.