Part of me says let the leaves grow in and you will probably not see the areas of concern. However if this is your long term landscaping plan then think and work strategically. Best long term practices indicate you should remove damaged or stubbed out useless limbs like shown here and in your pictures.

Pruning and Clean Up · More Info

Some like to fill holes with Dap Brand caulking. It looks better but there is some discussion as to the actual value. IMO if it can help keep water from pooling in those holes and turning it black then it would seem to be the lesser of the evils. Keep in mind it's at best a temporary measure as sooner or later the caulk will loosen and moisture will get behind it.

Pruning and Clean Up · More Info

Pruning and Clean Up · More Info

Envision how you get the plant to stand straight and start using stakes or other types of holders to systematically AND SLOWLY start straightening its posture. Some light pruning of select branches to begin shaping the trees can begin now and take several seasons to complete (IOW don't do it all at once but do it in phases over several seasons).

Secondary to your question but even more important based on what you said about the soil conditions in the container would be to pull the plant out and root prune about 1/2 to 1/3 of the ball and then replace the root bound material with more fresh mix. Matter of fact...root prune first as it's a great time to straighten the plant in the container as well.

I have a hard time thinking the plants are happy being root bound. There is some anecdotal discussion on Aztec Gold being very happy after years and years of being root bound. But I think that is at most the exception to the rule. Its likely any changes made last year will not be impacting the bloom cycle until this year so I would look for this year to be your benchmark.

The mature wood also has a unique bark pattern for a 16 year old plant. Kind of has a Windward side of the island look to it brought about by wet conditions. Not concerning in my mind but just an observation. For comparison purposes the plant in the DAP caulk image was around 15 years old at the time of the image

I had no idea I could groom the roots. Anything I should look out for? I am happy to do this and maybe they will fit better in these pots. I normally just use top soil or miracle grow potting mix.

You sure can prune the roots. On a plant that size i would root prune no smaller than a basketball size. My preference is to amend the soil with pine bark, perlite and/or pumice depending on what is available. Plumeria will handle most soil conditions except silt/gumbo/clays.

I have a Samoan Fluff which was roughly handled during a severe storm last year so its got damage all over it. I'll post a thread with pictures as I clean it up this weekend.