My "process" has been to clean window seal rubber with Meg`s Detailer Line D101 All-Purpose Cleaner diluted 3:1 on a Scotts Blue Paper Towel for larger black rubber seals and cotton swabs (AKA Q-Tip) on thin, narrow seals next to the window. Most neglected rubber window seals will blacken a cloth, whether it`s cotton or microfiber, so if you choose to use that media for cleaning, just be aware you will probably be throwing them away, hence my use of Blue shop paper toweling.
Another good cleaner is Illinois Tool Works-Permatex`s Spray Nine. That cleaner is more well-know as a nautical/boat cleaning product, but it works well on vehicles. What is "nice" about this cleaner is that is a disinfectant as well, so it works very well on mold and mildew without the bleach aspect. I found some at Walmart.
As far as protecting the rubber, I use Meg`s new "hybrid" Ceramic Trim Restorer or Aerospace 303 Protectant, again applied with Blue Shop Paper Toweling or old cotton cloths and Q-tips. I have never thought of using Klasse All-In-One (KAIO) for rubber seals. I have used it on B-Pillar posts (middle between doors) hard piano-black plastic trim pieces and black-chromed trim at the base of door windows with very good results. I also like KAIO for hard formed-plastic interior pieces, like center dash & instrument panels.
The typical "uninformed" vehicle owner kinda laughs at me when I detail the windows seals this way, but I have seen some older vehicles in this day-and-age of vehicles being owned and driven for 10 or more years where the window seals are weather-checked and cracked. A twice-yearly (spring and fall) cleaning and protectant application can greatly reduce this from happening and is even more important if the vehicle is not garaged or sits outside during the summer daytime.