The reasoning behind this being:
Our thinking was that on smaller sites, this should be handled by the site moderators on a case by case basis, rather than through an algorithm.
I see a few flaws in this reasoning:
Early betas don't have any moderators. When a user seeds an excess amount of questions there is no easy way to clean them up. While a site is in private beta a consensus hasn't even been built on when to close questions. (This has happened before.) As Jeff put it: "The fastest way to kill any Q&A site is to flood it with low-quality questions." Wouldn't this apply all the more for betas?
A possible solution to this as phrased by Anna Lear in a comment:
The community team monitors private beta sites and acts as moderators. If there's an issue with a user, flag one of their posts or make a meta post and we'll take a look.
Which gives rise to the following questions:
How does the community team know what is off-topic/not a real question? Sites can have a very specific subject making it hard for non-professionals to judge whether a question should be closed. Chances are the scope of the site isn't even properly defined yet.
Should these excess questions be closed? Users seeding a site don't necessarily have bad intentions. They can be overly enthusiastic without knowing the ropes of how the system works yet. After feedback the questions can turn out to be proper questions. Do you want to close questions which could belong on the site, just because there isn't enough time to handle them?
And finally possibly the strongest argument:
What good can come out of more than 6 questions a day? As in jjnguy's answer:
If you are asking over 2 questions per day, there is a good chance you aren't putting enough time into your questions.
Is it even possible to formulate 6 proper questions a day, follow up on them, and process the answers?
In my opinion an easier solution is the following:
Limit the amount of questions a user can ask per day on all sites. The monthly limit of 50 questions per month is probably less important, allowing a bit more free room for smaller sites (were this to be the reasoning). This alleviates all the above mentioned problems, giving moderators-to-be more time to address the issue before the site is flooded with unanswered questions.