BTO and reward points

We sell a cleaning item for like $11 that customers can buy regularly, and we are including it when they buy a machine.  We can set the price of the cleaning item to $0 but the reward points we can't change so the customer gets the free item and the points to go with it.  For the most part it won't matter since it amounts to like $0.22 but there are some machines that we include a lot more for free and the points add up.

Is it too much to add reward points to the BTO configuration screen?

Reward points are not necessarily based upon the selling price. If you have other products you always include for free then you could either :- adjust the points of the BTO product they are included with, or create separate instances of the products you include with zero points (although if you are tracking stock then that would probably not be a great approach). Adding extra tables in the database COULD be done, but personally I think the overhead of maintaining the data on those vs the relatively nominal cost of the points make it uneconomic to do so. From a software & support perspective it also introduces more complexity and risk of confusion. We could have gone straight for a percentage of total sale as a way of accruing points, but that offers far less flexibility than the approach taken, where you can boost reward points on certain lines and remove them on others.  There is no perfect answer on this as there is a trade off betwen complexity and maintenance and every store owner has their own idea as to the optimal approach for their business.
It is possible to customize the cart to accomodate what you are after, (zero points on products included with a BTO product).

Regarding the cancelling of orders you can and should adjust the reward point balance if you need to. That is accessible via the customer details in the admin pages.