Yes and no.
For example, Bandai had Monolith strip Xenosaga 2 of a lot of elements that Bandai wanted to save for the next game. They also fired Soraya Saga from the project, who was the lead writer, and is married to Tetsuya Takahashi. (Source, Soraya Saga's blog after she got fired.)
So when it comes to publishers being heavily involved in the development of an outsourced game, it really depends on how it is handled. When the ideas are implemented (sooner some times means less potential issues), and if the ideas are for the better, or worse.
This probably works best when there's proper trust between the developer and publisher, where both can express their ideas, without neccesarily enforcing them against the developers wishes.
Oh absolutely! Everything you said is absolutely true. Luckily Nintendo and Platinum Games seem to have such a relationship that you expressed in the bolded part of your post.
It is not just PG either, as we have seen them do good work with Ubisoft as well with use of their 1st party IPs in crossovers. It just seems like Nintendo is approaching these partnerships right, where maybe MS did not.
In any case, Nintendo and PG seem to be close enough now that it is almost reminiscent of Sony and Insomniac for example, before Sony bought them outright.