The method of generating stats is not a House Rule. It is one of many parameters which can be determined by the DM, at the start of the game. Rolling randomly is within the expected range of methods.
Likewise, taking the average for HP is an option, which may or may not be allowed on a table-by-table basis. Kind of like taking a Feat in place of increasing your ability scores, or allowing Gnomes in the game. None of these are wrong ways to play, and the game should remain playable in any configuration. That it's possible to roll a character incapable of gaining levels, because doing so would be instantly fatal, is an oversight.
When the DM deviates from the stated rules, it is a house rule.
Rolling 4d6 dropping the lowest and assigning as you wish, and the array of 15,14,13,12,10,8 are the two ways presented in the book and done so side by side with each other as an either or type thing.
Using the variant rule, point buy method is close to a house rule because of the variant status, much like using feats.
Any other method of character ability score generation is a house rule and the game can't be expected to take the use of them into account, that is the DM's job when deciding to make up his house rule.
Hit points are either a roll or take the average(round up) as the base assumed in the system, both presented as an individual option to the player that he can choose at each level. Anything else including demanding your players always roll is a house rule.
Not allowing gnomes, another house rule. But lets get back to hit points and negative Con modifiers.
If you use the rules as presented and the player manages to roll a 3 for an ability score (-4) modifier, and if he is silly enough to put it into Con and take a d6 hit die class like wizard, he will still be able to choose average(round up) in this case 4 h.p per level. Modified by his Con that is 0 h.p, not even a negative number. If the player wants to chance h.p, loss and rolls low enough on the d6 to get a negative number, that is his choice.
If the DM makes him roll for hit points, that is a house rule and again the rules of the game can't be written to accommodate every house rule at every table.