Rules also don't get used out of benign neglect rather than conscious choice. You see this both on the character side and GM side. So no, it doesn't have to be a house rule situation.
I don't see how that follows. A few definitions to understand what I am thinking.
a) All tables that are playing by the RAW will in the ideal be using the same procedures of play.
b) If a person familiar with one procedure of play goes to a different table where a different procedure of play is in force, he will perceive the difference as a house rule unless the person themselves perceives the differing procedure of play as RAW. The reason behind the differing process of play won't impact their thinking. Regardless of the cause of the departure from RAW, it's still a house rule.
Now, I suppose there could be some value in separating terms according to the different causes by which house rules arise, but for the purposes of this discussion since no commonly acknowledged terms of art exist to differentiate a rule created by conscious choice from a rule created by benign neglect, I see no reason to reject the idea that they are both "house rules" in the sense meant by the term (even if by benign neglect a table has never considered house rules to include rules created by benign neglect).
If we look at causes of house rules we find:
a) Deliberate departures from the rules because the GM/table finds those rules "wrong" in some fashion. They lead to outcomes that oppose (or are perceived to oppose) the tables aesthetics of play, whatever those are - too realistic, not realistic enough, too meta, departs from lore, too unbalanced, etc.
b) Departures from the rules because the GM/table doesn't not know the rules speak to the issue and so they inadvertently ignore the RAW through benign neglect, either not applying a rule or creating a rule in place of what the RAW specifies. It's not intentional, but a player from a different table will perceive this as a house rule.
c) Departures from the rules because the rules are misinterpreted from the author's intent for whatever reason without debate or awareness, leading to in effect a different rule being applied than the one that was written. It's not intentional, but a player from a different table will perceive this as a house rule.
d) Rulings where the rules are as being silent on a subject or else ambiguous to the point that multiple "valid" interpretations can be made and so a new rule must be improvised for the situation the rules are silent on. This is much more general than people realize I think, because so much of the metagame is usually assumed by the author of the rules, often unconsciously and so exacting procedures aren't described. A very common example is, "What do you do when a dice falls off the table?" Every table has some house rule for this in force. In this case 'd' though we do I think for the first time have an interesting property that distinguishes this category of house rule for them others and that is two tables can both be playing by the RAW and yet also both have differing house rules. Further note, that this category does have its own term of art, and I don't think that's a coincidence.