One of the down sides of taking a non ship tour is that the ship doesn’t wait if you are late getting back.
That is true but if you book with a reputable company, they will guarantee that you'll get back before the ship leaves. Think about it. If word got out on Cruise Critic or Trip Advisor that they did not get people back in time, their future business would be severely impacted.
What you say is a big selling point for the cruise line tours, but from what I read on Cruise Critic, the vast majority of people who miss the boat are people who go off on their own and lose track of time. I don't think I've ever heard of an organized tour getting back late, although I'm sure it has happened.
i'm currently organizing a tour in Guatemala for my upcoming Panama Canal cruise and have been concerned about getting back in time because I understand that traffic is an issue. The tour providers I'm talking to are highly rated on Trip Advisor and have told me not to worry.
The big advantage of doing a tour not thru the ship are a) they're cheaper, b) better tour, c) less people (often not a huge bus).
After retiring last year (and doing 2 cruises), we're up to doing 4 cruises this year. We did MSC Seaside in January (hated it), Holland America Koningsdam to Norway for 2 weeks (loved it), Oceania Insignia from NY (drive to port) next month to Newport, Boston, Portland, Halifax and Bermuda, and the Panama Canal cruise on Celebrity Infinity. That will total 46 days, which I'm OK with
. Next year we have two weddings so our 2 weeks planned in January may be it for the year.