It is absolutely essential to have a theory of system while implementing it. The software system itself, however, should exhibit only a simple subset of the whole theory in conscise form as possible. Because - usually the full theory becomes obvious only while writing the software. And, in practice, one uses only a tiny part for the implementation at hand.

I think one facet of this thing is that people have an ambition to build huge systems that encompass the entire universe - while in fact, most software system only need to utilize the already excisting capabilities in the ecosystem.

It's like since people are eager tinkerers they approach software projects with the mindset of miniature railroad engineers - while in fact, the proper way to attack the task should be as brutally simple as possible.

The reason huge theoretical systems are a problem in software engineering is that a) they tend to be isomorphic with things already existing b) while not implementing anything new and c) they obfuscate the software system through the introduction of system specific interface (e.g. they invent a new notation of algebra that is isomorphous in all aspectd to the well known one). And the worst sin is, this method destroys profitability and value.