I don't think there is anyIt makes no difference whether you use "the way" or "in the way" in meaning betweenthe contexts of the two sentences mentioned abovepresented. Usually But the use of the former is much more idiomatic and preferable. Besides, both phrases "the way" and "in the way" are interchangeablearen't always interchangeable; their use depends on the context.
'the way' is an idiomatic phrase, without differenceaccording to The Free Dictionary, that means "in the manner that". So if you use "the way" in meaningthese sentences, its use makes sense that's correct grammatically. For example
However, weif you use 'the way' to mean 'the manner', you can say he did it the right way or inrephrase these sentences as follows:
I was never allowed to do things the right way that I wanted to do them. He did
We have to make it (in)work the way (that) I likedthat we want it to.
The 'that' has been used here, "in" and "that" are optional i.e to mean 'in which". theyWe can be omitted. Nevertheless, the use of the phrase "in the way" is a bit wary. For example, if we say he did itthat to mean in the way I asked him, it sounds OKon, but if weby, or with which (The Free Dictionary).
You can also say:
I didn't likewas never allowed to do things the way in which I wanted to do them
We have to make it work the way (that) he did, thenin which we want it sounds a bit awkwardto. So I'll prefer
Look at the phrase "the way" tofollowing sentences in which the phraseuse of "in the way" so as to avoid any confusionisn't possible. Also, it is more natural and common to use
I like the way she dresses.
I hate the way she always criticizes me.
Look at another example in which "the way" instead of "in the way" isn't possible:
I take pride in the way my son helps the poor.
It'll not be outSo the use of place to mention here that"the way" and "in the way" is also an idiom used to meandepends on the context of a position obstructing something or someonesentence. For example Besides, he was standing in the waywhere they can be interchanged, I couldn't see him because of a crowd in the wayuse of "the way" is much more common and idiomatic.