In my corner of the U.S., examples #1 and #2 are very natural. However, the way we would express #3 is...
Does it cost anything?
If you need to use the verb "to charge," consider:
Will you charge me anything (for it)?
The reason I point this out is, in my locality, "charging" (a) is something that someone does for the sake of an aquisition, or (b) happens to an account or the symbol of an account (such as a credit card).
When you ask, "does it charge anything?" the subject is "it," but an "it" can't charge anything (it can be charged, but not do the charging). "It" is the reason for the charge. Implying that something else is being charged is complex because the relationship is important, so we expect to know who's being charged.
As I sit here and think about it, Example #3 is (for my locality) asking if "it" can make a charge, as if you were talking about your bicycle making a purchase at the grocery store.
Remember, that's a location-dependent observation.
HOWEVER
You will find examples of anthropomorphization (where an "it" can do something) with some issues. The most common example is the issue of gun ownership in the U.S. It's common to hear the refrain, "guns kill." Obviously, a gun, sitting on a table, can't kill anyone without someone or something being done to or with the gun. (The common counter-refrain is, "guns don't kill, people kill"). I bring this up as an example of when you can find "it" doing something that, normally, "it" wouldn't or couldn't do.
English, there's always an exception.
Both are completely natural, but imply different ways of looking at the spatial orientation of the elements.
"In the same plane" is probably the more accurate from the mathematical perspective, since a plane has no depth. A point cannot rest "on" the plane the way a cup would rest on a table, since that would mean it is above the plane and therefore not part of the plane.
However, "on the same plane" is a common expression. Even though they should know it represents a mathematical fallacy, mathematicians persist in using the same language to describe these spatial relationships that they would use for real-world objects.
So, use whichever sounds better to you.
Best Answer
There is a difference between having a color and being a color.
To be a color is to be entirely, or predominantly, of that color (e.g. a blue sky). If more than one color predominates, then an object can be multiple colors (e.g. a red and white striped shirt). In contrast, to have a color is less exclusive; it suggests that other colors may be present, and those other colors may even be more prominent than the one you are talking about (e.g. the flags of Taiwan, Saudia Arabia, and Slovenia all have white on them).
To offer some real-life examples using Wikimedia Commons images, if you asked the average person what color these tulips are, the response will most likely be yellow, or some variety of yellow:
The flower below is trickier.
If pressed to name a single color, most people would also say this tulip is yellow, since the overwhelming proportion of the visible parts of the flowers (i.e. the petals) is yellow. From a distance, it will appear entirely yellow. But many will at the same time object that the flower also has red in it— it is yellow with red stripes or is yellow, but has red stripes.
In this third case, many may refuse from the outset to identify the flower as being any one color:
They will say it is purple, white, and yellow, or that it is white and purple and has yellow (on one petal). This flower has yellow, but it cannot be said that it is yellow.
In practice, to say flowers can be many colors and can have many colors is nearly equivalent. But one could draw a distinction between the two. To say flowers can be many colors is to say that flowers may reflect a range of predominant colors. In contrast, to say flowers can have many colors is to say that many colors can be found among the flowers, even if they all share the same predominant color.
Thus, if flowers can be yellow, you can expect flowers looking like the first or second examples. If flowers can have yellow, you can expect flowers looking like any of the three examples.