Since the binary numeral 100 represents the value four, it would be confusing to refer to the numeral as one hundred.
What you have here is a 'hidden' conditional construction—although there is no express if clause, the infinitive clause serves the same purpose:
It would be confusing to refer to the numeral as one hundred.
It would be confusing if we referred to the numeral as one hundred.
This sentence employs past forms not to move the time reference to the past but to characterize the statement as imaginary, hypothetical or unreal, where present forms characterize the statement as a real-world probability or certainty.
PRESENT: It will be confusing if we refer to the numeral as one hundred.
.... ↓ ↓
PAST: It would be confusing if we referred to the numeral as one hundred.
The author has no intention of referring to the number as 'one hundred', so he employs past forms.
Past forms are used this way with all verbs, not just modals like will/would—note that refer changes tense, too—but it is especially marked with the modals because modals express possibility and probability, and are therefore intimately involved with imaginary, hypothetical and unreal situations.
There are, by the way, yet more uses of will/would; but cataloging those would not help you understand this use, and would make the answer run for pages and pages!