I wouldn't say that your sentences emphasize the preceding subject. (You don't actually provide a preceding subject in your examples.) Instead, the first part of each sentence serves to introduce the second part.
In both of your sentences, the first part is mostly extraneous. Each sentence could be shortened to be more direct by simply removing the first part altogether:
A, B, and C need to be fixed.
A works like this and that.
Phrases like "the real issue is that" and "what happens underneath the hood is that" may help with the style of the sentence, but they aren't adding anything to the essential meaning of what's going on.
They are similar to:
By all rights . . .
In other words . . .
If you look at it more closely . . .
If you're worried about your sentences being too "wordy," strip out these introductory phrases—then step back and ask yourself which sentences don't need them and which could benefit the surrounding text by having them.
You can also use shorter introductory phrases like but, in reality, however, and so on.
This is not to say that is that phrases should never be used, simply that they don't always need to be used.