Why are there work crews occasionally on your roof? Is it a multi family building?

Yes

Presuming you will know when someone is up there, you could install a remote controlled shade to close when needed.
Skylight shades

sorry, I cannot edit my post above...they also make manual shades that you can close with a pole, if you can reach them. The shades fold up to being nearly invisible when open. They also make reflective film that would block the view into the room in the daylight. It won't work at night when the lights in the room might be on, but presumably there won't be a night shift working.
Reflective film for skylights

We have opaque skylights which let in a nice indirect light without harsh sun or shadows. (Way more flattering in the bathroom too). Benefit is no inadvertent flashing or peeping.

Opaque sounds like a possibility. We'd have to get approval to replace the clear glass.  We're in a multi unit building. No advance notice before the work is done but it's usually in the morning so the idea of reflective film is also of interest. Thanks for the ideas. The other issue with toilet is that it could be seen from the landing inside the bedroom but that doesn't hit me as a concern, would it be for others?

looks like you could flip the location of the shower and toilet/vanity and the toilet would be tucked away out of view.

Yes it could be flipped, shower vs. vanity toilet. But I would still have potential visibility, now into the shower,  and would lose natural light at the mirror. Dilemma.

We are looking at a pocket door - or in this case, 2 doors on a railing, both able to open and close. Hoping that's doable. I have two old Chinese doors that I would like to use.

You don't have to replace the skylight glass. They make opaque film that goes right on top of the glass. 3M makes it and they professionally install it. I know because I've used it in several places in my house including all the windows in my garage.

Here is a clear glass door to our elevator, with 3M film I had put on. I wanted it only semi-opaque but they make film even more opaque. And they make film that is one way as others have suggested.

This is good to know - I thought it had to be installed as opaque. Thank you, this is a big help.