Is it better to roll over a budget manually or allow it to work automatically

Well that is sort of a personal preference/use case kind of question where there isn't really a "right answer".

I definitely agree that the very fact that the reports don't support them makes it an even harder decision to use them or not.

But if one is going to use them the first step would be making sure it even makes sense to use a rollover for that category.  If you know you are going to pay exactly the same amount each month for rent for instance, you wouldn't want to use a rollover on that category.  It gets a bit harder to decide for those bigger expenses like paying for car insurance twice a year.  I personally don't use a rollover for this, I just put in the amounts on the months they are paid.  But others "save up" and want the rollovers.

The other "use" for rollovers is for things that you know you spend "on average $XXX", but not consistently for any given month.

Once you have an idea of why you would want a rollover on a given category then I think you can make a better decision on if you want change the rollover amounts at any given time.  For instance some people want to reset them to zero at the beginning of a year, and others don't because in reality that isn't how the world works.
And the truth might be you reset some and not others.

It is like the statements where people want to budget to a certain interval (usually to match their paycheck), but their bills are never going to "agree to this" and just line up.  Sooner or later you have draw money from "savings" to make up for the fact that the money might come in, in one "interval" and be spent in another.