IIRC, all those areas were heavily mined and/or fortified against the amphibious assault? Thus it would not be possible without a good deal more preparation, plus the Germans did not really have a good enough doctrine of amphi operations to try it?
Furthermore, the AG North proceeded to reach Pskov on July 2nd, barely two weeks into fighting. Seeing that Tallin managed to hold until September, it is hard to imagine any seaborne assault the Germans could have attempted. But maybe, as you say, it was worth a try?
IDK how mined they were (or were not). From the description of the evacuation of Tallin, it seems the Germans were the ones doing the mining.
Regarding their ability to carry out landings, these would be mostly re-runs of the ops they carried out against Norway, which went off pretty well, all things considered.
Also, Tallin fell as late as it did because the Germans were busy advancing elsewhere. Here, if it's taken in a coup-de-main, it can be used to ferry in supplies far closer to the front.
The beauty of all of this is that, if at any point it fails, the OTL plan for AGN can still be taken, and losses would amount to only the paras that were lost OTL anyway, a bunch of infantry used in the landings and some ships (which were useless as far as the campaign against Russia was concerned).
If it works, you will have taken Leningrad along with its port, which means all the trucks etc used OTL to supply AGN can now mostly go to AGC.