Border crossing

Pretty sure it does not matter how/where you exit the Schengen zone, the process will be the same. If it's not the whole system is useless.
Your departure from Croatia will be recorded, so that when you go to re-enter the border guard will know if you have used up your allowable time for the type of travel document you have.

Whether you drive across the border in a taxi, rental car or bus the procedure will be the same; they will do the same thing as flying from Paris to New York.

Last year we visited Bosnia by flying into Dubrovnik, getting a taxi across to Mostar, and then later flying home from Sarajevo. I just checked my passport and I was stamped when arriving in Dubrovnik airport and departing from Sarajevo airport, but looks like they did not stamp it when we crossed the land border. We did stop at a border station where they checked our passports but no stamp. Note this was a border crossing close to Dubrovnik so you will likely use a different crossing where they might do something different. You might also be able to request that they stamp it?

In late 2023 I was on a tour by bus that went from Croatia to Montenegro and back, then Dubrovnik to Mostar (following standard route that takes you north up the coast for an hour or so, then turn inland into Bosnia), then back into Croatia much further north. At the Schengen boundaries passports are carefully checked at two border posts (one for each country) and I got so many Balkan stamps that I had to renew my passport early before my next trip because it was so full. As Europe moves towards all electronic systems that make passport stamps redundant, you may not get as many stamps as I did then, but this will not be a problem, your crossing will be documented.

Your passport will be checked. Insist on a stamp. Never hurts. But also know your passport info will be entered into the Schengen system both coming and going, even if they dont stamp. Its the system that track compliance. Guards dont look for stamps and do math.