This is an insightful question because you have struck upon a property of integral calculus. Your example demonstrates how, by taking infinite limits, we can create transformations from an area to a line.
In the words of Jyrki Lahtonen above, "The property of a shape to be a rectangle is not closed under taking the limit." What this means is that the taking of limits of a rectangle's properties has the power to transcend whether it is a rectangle or not.
However in your example this capacity to become "not a rectangle" does not derive from the $0.999...$ approaching $1$, it derives from the width approaching zero.
You should take care to define $l$ in your numerical format. l can be written as a function of the number of 9's in your sequence, as follows: $$l(m)=\sum_{n=1}^{m}{9\times10^{-n}}$$
And you are defining $e=1-l$
To state that $0.\overline9=1$ is equivalent to stating $$\lim_{m\to\infty} l(m) = 1$$
The area of your your rectangle is $e\times l$
And you are stating that $$\lim_{m\to\infty}( e(m) \times l(m) )= 0$$
This is clear because the limit of $e$ is zero, the limit of $l$ is $1$ so the limit of their product is $0$.
Therefore the limit of the area of a rectangle, as its width approaches zero; $m\to\infty$ is zero.
Which as you correctly postulated, implies that a line segment can be thought of as the limit of a rectangle as its width approaches zero.