I read through this post and the great feedback you have been getting. I don't know if algae is a problem, but it would concern me too. Your roots are looking great and seeing that healthy root that already hit the bottom of the bottle, I personally would repot into a small pot.
I live in Southern CA, so my weather conditions are different than yours. Cold is more of a concern than rain. Plumerias grow naturally in hot, humid and rainy conditions. Remember, I also don't get as much winter rain as you do and no summer rain. My winter nights are generally in the 50s and occassionally in the 40s and I never bring in my potted plumerias because I have too many. Again, I don't have winters like you do or even like Tarev does in Northern CA.
I root my plumerias in a mixture of perlite and pebbles. In a local gardening group I belong to, one of the members mentioned that mixing lava rock into their potting mix of 1/2 cactus mix and 1/2 perlite has made a huge difference in their plumerias (very healthy and lots of blooms). It makes sense since plumerias grow on tropical islands that have volcanic rock as their base. In the future, I will root plumerias in a mixture of perlite, lava rock and pebbles.
I mix my own potting soil of perlite, pumice and peat moss. In the future, I will be adding lava rock to the mixture, even though technically perlite and pumice are lava rock. I don't get root rot with that soil mixture. I put compost on top of that layer and then cover with a wood chip mulch. I remove the wood chip mulch from my potted plumerias before winter for fear of it causing root rot with the colder, damper weather. This spring I did lose a plumeria to root rot because I used too much compost on top (1/2 my soil and 1/2 compost in a 5 gallon pot for a Jungle Jack's Divine dwarf tree.)
Also, just an FYI, orange plumeria flowers need a lot of sun and heat to get that beautiful orange color. I have a no ID orange plumeria that grows yellow flowers until we get a heat wave. Hopefully you have better luck with your hot humid summers.
Please let me know how your roots look when you repot. For me, young roots grow around a sandy mixture and not through it. I'm curious if your roots are growing in the middle of your bottle container thru your sandy perlite mixture.
