While one could fudge the ZC code to force auto-incrementing by 1 regardless of the server's global setting, in your multiple-master situation, that is indeed likely to cause replication conflicts ... and then you'll have an even uglier mess on your hands later.
They probably think that multiple-master is the "safest" way to do things because it doesn't require that customers rewrite all their PHP code to work in a master-slave format. And, while it's true that there's no PHP code rewriting needed to use their multiple-master-solution-by-fudging-autoincrementing, there IS a BIG downside: the very problem you've reported ... gaps in record numbers when the code is designed to work with database-driven incrementing dependent on using auto-increment values instead of more complex methods like building custom triggers and stored procedures.
It also means your Zen Cart tables can only store half as many "maximum number of records" as they're designed to hold. So, you may have to eventually alter the db schema to allow for much larger field types on the fields using auto-increment properties.
It would be MUCH safer to have a proper master-slave setup. But that requires rewriting the PHP code to do SELECT statements from "slave" servers, and do INSERT or UPDATE statements on the "master" server only. And rely on scheduled replication cycles to keep both servers updated in "almost-real-time" (which is adequate for almost everything).
Zen Cart v1.x is written to assume a single-master-only MySQL server configuration. And, IT DOES WORK FINE in your host's odd autoincrement situation, but you will have to put up with the gaps in numbers all over the place. (order numbers, customer numbers, zone numbers, product numbers, category numbers, order-status-numbers, etc.)
Zen Cart v2.x (currently under development, not ready for viewing) is written to support master-slave configurations, and also has a number of things built-in to insulate against things like your auto-increment anomaly ... well, for order-numbers anyway, but not yet for other data records.
We'll add a task to explore handling those differently for cases such as what your hosting company has chosen. But it won't likely get backported to v1.x because it would require sweeping code changes on both catalog and admin sides.