When I used a Zombie Spawn Egg and I tried to kill them using /kill @e[type=!Player], I discovered that all the entities died but me and the Zombies I've spawned. So I tried to execute /kill @e, but they were still alive. Nevetheless, I could hit them till death.
It also works with any command that uses target selector and with any mob.

In the attached images, I did the same but using renamed pigs and a saddle, to make it more graphic.
As you can see, the first one is a pig spawned with /summon. It's like a natural spawned pig and the saddle is just to mark him. The second one is spawned using an egg. When I execute /kill @e, all entities dies except the spawned with egg.
Then I tried /tp @e DanielFerG_, but "That entity cannot be found". Finally, I typed /tp @e[name=SpawnedWithEgg] DanielFerG_ and the same happened.

I've tested this by using a real naturally spawned mob and a spawned egg mob, no renaming it, and the result is the same.

Hope I have been helpful. Cheers and I hope we will receive hugs! ^u