Common names of plants are a very unclear matter. There are big differences not only between languages, but also regional differences within a single language.
There are lots of (closely related) plants which are sold under the name blueberry. And probably not even the person who grew (or gathered) them can tell you the exact species. While it does matter when it comes to jam (for the same reason it matters whether you use Roma tomatoes or Cherry tomatoes for a sauce) it is highly improbable to find a source which can consistently provide you with a specific known variety. Also, you probably have to study some very specified botanical literature and be provided with parts of the plant other than the berries in order to be able to identify the type with some degree of accuracy.
On the other hand, don't let that come in the way of good jam. Blood orange marmelade may taste different than bitter orange marmelade, but both are good. The same goes for blueberries: you can use any variety, even if some of them would be a bit better on their own.
What you need for a jam is a good sweetness to acid ratio, the proper amount of pectin, and as much aroma as possible. A softer texture also helps to prevent unpleasant lumps. So generally, you want to go with the ripest fruit available. They are soft, and have the fullest aroma. This is something you might want to consider with your current source of berries: maybe they're not a special "green on the inside" variety, but only underripe. If they don't taste very sweet, and their aroma isn't very complex, I'd try to find other sources. Farmer's markets and organic stores are usually able to sell much better fruits (because they cater to a picky, price-inelastic clientelle), but of course they cost a lot too.
Sweet fruit is always good, but you need enough sugar added for food safety. A ratio of 2:1 (fruit to sugar) can still be kept in the pantry, more fruit than that and you need to refrigerate the unopened glasses too. With blueburries, you'll need to add both pectin (to get the jam to gel) and acid (to get the pectin to work). This is the part which will vary with fruit variety: more watery types will need more pectin, and less acidic types will need more acid. If you want a good quality jam, you'll need to do some experiments until you get the proportions right. If not, you can buy "jam sugar" or however it is called in your country - this is sugar with pectin and acid already added. It won't have the perfect ratio for your fruit, but it will more or less work. But then, if this quality is enough for you, you can skip buying the expensive berries and slaving at the stove, and buy manufactured jam.
you could try some other thickeners, like xanthan gum, tapioca starch, arrowroot, or the like. not certain of the proportions, though, but i'm betting google knows.
Best Answer
The story is more complicated than SAJ tells it. Blueberries, like many other purple foods, are colored by a pigment called anthocyanin. It changes its color from red at very low pH to real blue at very high pH. At the blueberry's natural pH, the color is a purple with more red than blue in it.
What you can do is to juice some blueberries separately, then add lots of baking soda to the juice. It will turn a dark blue. You can then mix it into the batter.
The problem is that you will be changing the taste of the muffins, and some of their rising behavior. If you use little enough blue-turned juice to not make a major change, you will get dirty greenish muffins, as the batter itself is yellow-beige, and that will mix with the blue. If you use enough to color them, you will have pretty display muffins (provided they don't stay flat because you turned the batter too alkaline for the baking powder to work) which will taste like soap.
Personally, I will stick to food coloring. "Natural" coloring is an unachievable utopic for most foods, as natural pigments are finicky and almost never concentrated enough to color a food flavor with them. The only time they work is when a food is made predominantly from the coloring food, e.g. blueberry sorbet is indeed red-purple from the blueberries contained in it.
This is an example of naturally colored shortbread cookie dough. The lavender dough was colored using elderberry fruit juice with lots of baking soda. It was very noticeable in the taste, I wouldn't do it again. Ironically, the slightly soapy taste fit a bit with the lavender aroma, it was just weird eating the stuff.