Actually it does, if Kakashi knew nothing about Oro's seal then he's basing his analysis off of Naruto before Orochimaru seal which still was poor chakra control. Ebisu, who was informed by Kakashi said this about Naruto's chakra control
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. Kakashi's analysis of Naruto's skills would be from what he observed on their missions before the Chunin exams and there's no reason for him to think Naruto's chakra control is going to increase or decrease in the forest.
You're example with Itachi isn't the same since Itachi was sick for years and we were introduced to him already with the sickness. Naruto got his chakra sealed then
Kakashi only saw Naruto fight once and that was it Kiba where he used Shadow clones and transformation jutsu. As you can see from Kakashi's/Ebisu's analysis, Naruto would use a ton of stamina to make fewer chakra which tires him out, that wouldn't change after Naruto got Oro's seal but make Naruto use even more chakra to use his jutsus but Kakashi wasn't using his Sharingan to see Naruto's chakra nor did he see Naruto in multiple fights as he had in the land of waves.
Oro's seal disrupted Naruto's chakra flow so Naruto's chakra control was off balance from what it's normally was. Oh and Naruto with the seal actually was learning to walk on water much faster than Ebisu thought he would and this is without him knowing about Oro's seal
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. So Naruto's chakra control is actually really good if he can learn it right after being told how to do it and with his chakra disrupted.