make something clear is an example of a phrasal verb - a verb plus a particle p. p is normally an adverb or preposition, but in this case it's an adjective. Some phrasal verbs can exist in two patterns: the usual pattern is N+V+N+p but sometimes the pattern is N+V+p+N. Examples might be:
I looked his name up
I looked up his name.
The usual form is make something clear, and this is used when something is just a few words. If something is a complex noun phrase, we get uncomfortable about the distance between make and clear, especially if the noun phrase could cause misleading parsing, for example make the difference..., so we move make clear together and put the noun phrase at the end.
For personal pronouns like it, the first form is always used and a short noun phrase like the example below is probably still OK using the first form.
...make the reason for his actions clear.
It has to get to something like the two examples below before we start to favour the at-the-end approach.
make the difference between right and wrong clear.
make clear the difference between right and wrong.
Looking at the second example that you quoted, both analyze and make explicit apply to the noun phrase (highlighted), so the sentence would not make sense if the noun phrase were in the middle:
We analyze and make explicit the model properties needed for such regularities to emerge in word vectors
Note also that the noun phrase is a lot more complex than you indicated, so even without the analyze and complication, the at-the-end approach would not only be grammatically correct, but would be the preferred option. Here is a real example:
In this study, we make a simplified mathematical model for the ladder of van der Pol oscillators coupled by inductors in order to make clear the mechanism of the generation of the wave-motion. Proceedings of the IEEE
This NGram shows that make it clear is not so far ahead of make clear the... in terms of frequency of use in writing. You can look at the actual instances to see further examples of noun phrase usages.