You're kind of asking the wrong question. How to color food-safe silicone is the simple part. You just add food-safe colorants. There are companies that sell these, like Colorsoul, a Chinese company, sells LSR liquid silicone colorants, some of which are food safe silicone additives when properly used.
The hard part is in the definition of food-safe or other kinds of "safe". It isn't food-safe because you make it from components that are food safe. It's food safe because you convince the appropriate government regulatory organization that your finished product meets their requirements for being labelled as safe for a specific purpose.
There are different kinds and levels of "safe", with different requirements. For example, medical devices, infant bottle nipples or teething toys, food storage for various types of foods and storage conditions, temporary food contact, high-temperature cooking utensils, etc. It can be expensive to meet these regulatory hurdles (and even more expensive if you don't).
Also, a "food-safe" (or other kind of "safe"), label applies only to the specific type of use you get it approved for. So you couldn't get approval for a utensil that will be in temporary contact with food, and then make nose plugs out of the same material and claim they're safe for that purpose.
Making something that you can claim or imply is food-safe, and sell legally and with limited liability, generally isn't within the financial means of a hobbyist occasionally making them in their basement. It requires a substantial investment that would normally be amortized over a lot of production on a commercial scale. And the colorants are sold in quantities appropriate to that scale.
To better address the clarification added to the question and discussed in comments:
If you will be making these items just for use by yourself and your family and friends, won't be selling them, and they don't pose a clear and present danger to the public, the government won't come after you, and your friends probably won't sue you if they get sick and understood the risks. People are free to put anything they want into their mouth and other orifices (nose and ears are some examples of other orifices).
So you can use any basis you want to define a level of safety you're comfortable with. Say it will be adequate to just restrict the materials to substances that have been certified as usable in food-safe end products, and you will judge proper curing by the physical characteristics of the finished item (does it feel properly cured, no odor, no surface residue, etc.). Just use colorants that are sold for use in food-safe products.
The LSR, mentioned earlier, is one. But you could also contact other big makers of "food-safe" silicone or colorants, like Smooth-On, to inquire about which of their products might be suitable. Making products sold as food-safe is normally done on a commercial scale because of the costs involved; that's the audience and market for the colorants. So sellers of the colorants don't advertise them to the public or sell them in small retail quantities for hobbyist use.
You could also use pigments that aren't harmful and may be more readily available. For example, colored mica is used in things like eye shadow, which needs to be safe enough that people won't be seriously harmed by accidentally getting some in their eye or ingesting a small amount. It takes very little of it to color silicone, it gets permanently contained within the silicone, and nothing leaches out of it when exposed to water or substances in food.