The only thing that was contradicted was the idea behind Goku and Zamasu being on par with Beerus and even that wasn't a contradiction. As you said, Gowasu made those statements based on Beerus' claims and Beerus corrected him because he clearly misunderstood. Beerus' acknowledgment of Goku being a formidable opponent who can stand up to a God of Destruction is a reference to what the readers knew. There's no reason for bringing this up if it served no importance to the narrative. That counterexample is interesting but Beerus and the viewers are privy to what transpired in Battle of Gods. Beerus acknowledges SSJ2 Goku as one who can stand up to a God of Destruction so his feats in Battle of Gods still hold merit.
It was contradicted because Gowasu retracted his own comment, Goku and Zamasu can't be on par with Beerus since that would make Goku and Goku Black many times stronger than him. I can agree at some exent that Goku can be a formidable opponent to a God of Destruction, but talking about Goku of this arc and in general, not limited to one of his weakest transformation. SSJ Goku had God Esscene against Beerus and Goku didn't felt any weaker than before even after his time limit expired.
It's implied that when characters fight head on against their opponents they understand their level even better, such as when SSJ2 Vegeta fought Kid Buu:
Chapter: 511 (DBZ 317, P8.2)
Context: as pure Boo beats up on Vegeta
Vegeta: "
Wh-what fast and heavy attacks...! ...Kakarot was... fighting with a gu-guy like this...?!"
In this case, Trunks felt how heavy were Vegeta's punches and then come to the conclussion that just SSj Blue can stand up to the God of Destruction:
Episode: 54
Time: 18:53-18:55
Context: While getting beat up by Vegeta
[F] Trunks: "He's strong... Far too strong!"
It's important to notice that this is the same Trunks that observed SSJ3 Goku stopping his strongest attack with his fingers and then proceed to one-shot him.
I don't disagree, but it is still embedded in the scene. Gowasu expressed doubts about Goku and then upon Goku overpowering Zamasu, Gowasu retracted those doubts. Consider this, if Goku didn't surpass the level of a mortal and reach the level of the gods with his Super Saiyan 2 form, would Gowasu actually believe Goku stood a chance against Beerus? It's illogical for that to be the case had SSJ2 Goku still remained at a mortal level.
Mortal level is relative, unless you are talking about an specific mortal level, there are mortals too strong, as well as too weak... Hmmm, I don't know, Gowasu can sense ki, but can't sense Beerus' properly...? That's what I imagine...
Yes. Those examples would include Hit and Final Form Frieza. Kuririn states that even both him and Gohan were in "top condition" which pertains to Gohan's "Ultimate" form, there'd still be nothing they could do. Frieza even acknowledges that Base Goku was much stronger than Majin Buu. Even if you deny that Goku was god-level, there are still clear parameters that established that Base Goku surpassed all of Z save for Vegetto I guess.
In regards to the Toei filler, the difference is that Toei had the creative liberty of doing whatever they wanted with the anime filler. When it comes to Super, Toei can't do whatever they want. Toriyama had to approve their work and he approved of the idea that Base Vegeta could trounce SSJ3 Gotenks. That remains consistent with how the Base Saiyans were portrayed in Battle of Gods, Resurrection F, and Goku's battle with Beerus after the U6 Tournament.
How? Goku was able to make a wound on Hit, even though, this same Hit could make SSj Blue Vegeta bleed with his punches, plus, Goku didn't get that damaged which already confirms that he is opperating a very reduced level, Base Goku's performance against Hit isn't anything to go by.
When it comes to Final Form Freeza, well, his level is changeable and isn't consistent from one way to other, however, if we want to justify his case quite a bit, Goku needed to kill him in a very weakened state using a Kamehameha in SSj Blue, even though, SSJ or even base would've been sufficient.
Super and Z treats Ultimate state differently, so, it mostly referrs to his current condition which was a pretty bad one. Freeza doesn't know how strong Majin Buu is, and the only thing he knows is that he could never provoke him or Beerus, which means that they were far superior to him.
The Z Filler which was preserved in Kai of him observing fighting SSJ3 Goku and Kid Buu, seems to be retconned, as hell is potrayed different, even then, to think that he could grasp them, when his memory is limited to the
weakest SSJ it's clearly too much of a stretch.
If we go by "Toriyama approved", Toriyama approved Bulma slapping Beerus, as well as many fillers or retconned his manga of the Gohan and Trunks' story changing it from the anime, don't know how that could end...