WHile I understand it can be house ruled - I consider it quite iffy this 'leadership from boats'.
I think only the US had 'Command Ships' structured and staffed to lead ground operations and that was for their Island Hopping campaigns in the Pacific.
Here it just seems to me it's a way not to keep the HQ (with precious leader?) at risk, and eluding the stacking limits.
Given in my own game as Soviet I just kept the HQ on the ground in the pointe of the other peninsula.
But this is applied to Riga, Talinn, etc - and as it is now to 'sink' things is virtually impossible even if savage Naval Patrol is ran over the hex.
I remember I tested some naval movement business and something Russian on a sea transport can even get to the hexes outside Stettin or Konigsberg and sit there unmolested.
So while it is definitely easire to house rule Amphibious Invasions, til something is coded about distance from ports or so - this one can be quite obscure to notice.
A simply fix is IF a ground unit is Embarked, it provides no SU units and has all Stats reduced to 0 (or automatically fails all tests).
It's fine and fair to have a General taking a cruise on the sea, but from there to exert command operations ... that's another story.
Either the General is evacuated from the sea-pocket OR it is kept there with all the relevative issues.
If someone wants their HQ in Talinn for instance - either they have 2 units + HQ, or get their City Fort for APs, or simply do not have it. Etc.
I believe the naval HQ too is iffy - I mean, if that is the Black Sea fleet, the Luftwaffe would be sinking their capital ships quite fast.
It's not like Dunkirk that it's small ships that are getting in and out to get soldiers. It's big naval guns coming in - DD / CL / CA type of size.