You are right; the word processor's algorithm has basically run out of its capacity and is falling back on synthetic rules, which language doesn't always follow.
For instance, it is undeniably correct to say:
A lot of people are in agreement.
A lot of people is in agreement.*
Your word processor will probably get this one right, because it has some pattern rule which takes into account the behavior of the term "A lot".
Without such a rule, if we fall back on the synthetic application of rules, we are led to the conclusion that "is" is the right verb. If we stick in parentheses, we get this:
A lot (of people) is ...
Clearly, a "a lot" is one thing, which is why the article "a" is used. That lot is modified by "of people": it is one lot, containing people, right?
Basically, in your sentence, "as well" just serves as a conjunction for the sake of variety. You might as well have written:
An angular threshold, and a few distance and height thresholds are basically used for the reconstruction.
Whether the "as well" clause is extraneous to the sentence, or whether it is just a conjunction in a list, is quite ambiguous. We can parenthesize it equally well like this:
An (angular threshold as well as a few distance and height thresholds) are basically used for the reconstruction.
Your word processor's grammar checker neglected to explore this parse, and only processed this one:
An angular threshold (as well as a few distance and height thresholds) are basically used for the reconstruction.
Ignoring the other parse is only justified if we put in commas:
An angular threshold, as well as a few distance and height thresholds, is basically used for the reconstruction.
But even now, "are" can still be used, for the same reasons that utterances like "a lot of people are" or "those two are a funny pair" are correct, dispensing with agreement based on apparently plurality, and going with semantic plurality for the verb.