You are visualizing vectors as "free vectors". I've never seen a systematic elementary exposition of how to deal with them. Illustrations in physics books sometimes draw vectors so their "tail" doesn't begin at the origin of the coordinate system. That type of vectoris called a "free vector". All the common formula involving cartesian coordinates of vectors assume that the "tail" is at the origin. This is the standard way of treating vectors. They are "bound" vectors.
If you regard the vector between the points (3,5) and (4,9) as (1,4) and you regard (1,4) as referring to vector whose tail is at (0,0) and whose head is at (1,4) then (1,4) does not lie on the line segment connecting (3,5) to (4,9). In fact, if you are only using 2 numbers to represent a 2D vector, then you don't have enough numbers to represent both the head and tail of the vector.
Likewise, if you are using 3 numbers to represent a vector in [itex]R^3[/itex] you can't represent both the tail and the head. When we say "a vector in [itex]R^3[/itex]" , this is usually taken to mean "a bound vector specified by 3 numbers insead of a free vector specified by 6 numbers.
In terms of bound vectors, a plane in [itex]R^3[/itex] not passing through the origin can be represented by taking all the vectors that lie in a given plane that does pass through the origin and adding some constant vector [itex]V_c[/itex] to them.
When you ask about a linear combination of vectors , you have to specificy what vectors we can use in the linear combination. A linear combination of "bound" vectors is always a vector whose tail is at the origin. Multiples of a "bound" vector never lie "in" a plane that doesn't pass through the origin..