When you pay, you're told you will be charged again on the first of the following month--that goes for if you're pledging on the 1st or the 31st. So yes, if you pledge at the end of a cycle you'll get charged twice in succession.
But!
Most creators have an archive of content behind that paywall you were just granted access to, and many even organize the content by tags. So your first payment is like being granted access to that archive. If you weren't charged until the following month, still got the archive of content you were pledging to pay for in the future, and skipped out before the first of the month--that creator gets nothing, and you still got access to their content.
Source: I've had a patreon for nearing 3 years, most of it under a pay upfront system. Have had zero surprised patrons regardless of when they pledge.