Steven has given an excellent answer, but I fear many people will not read all the comments and decide that the answer is basically no instead of yes due to the loss of a canonical form of continued fractions.
I will now try to demonstrate how to go about finding a good representation for base-$\phi$ square roots and why this might be useful.
It turns out that the sine or cosine of any integer multiple of $\pi/60$ can be represented as a linear combination of the following 6 factors (see Exact Trigonometric Constants):
$1$
$\sqrt 2$
$\sqrt 3$
$\sqrt 5$
$\sqrt{5+\sqrt 5}$
$\sqrt{5-\sqrt 5}$
Except for 1, these are basically quadratic extensions of $\mathbb Q$.
I want to represent a subset of the constructable numbers that use only sines and cosines of angles
$\dfrac{n\pi}{60}$ where $n \in \mathbb Z$.
Generalized continued fractions (GCF) allow me to represent square roots using the following formula (see Methods of Computing Square Roots):
$\sqrt z = \sqrt{x^2 + y} = x + \dfrac{y}{2x + \dfrac{y}{2x + \dfrac {y}{2x + \dfrac{y}{\ddots}}}}$
where $x$ and $y$ are positive real numbers, thus guaranteeing convergence as long as the product of successive $2x$'s grows faster than the product of successive $y$'s (see the Convergence Problem). Generally we want $x$ to be as large as possible and $y$ to be as small as possible for faster convergence.
For $\sqrt 2$, $x = 1$ and $y = 1$.
For $\sqrt 3$, x = 1 and $y = 2$ does not converge quickly. Let's take a look in base-$\phi$.
$3 = 100.01 = \phi^2 + \phi^{-2}$ so $x = \phi$ and $y = \phi^{-2}$ will give much faster convergence. You might wonder if $\sqrt 2$ has a similar faster convergence, but as $2 = 10.01 = \phi + \phi^{-2}$ we don't have an easy way to represent $x$ as $\sqrt \phi$. If we re-write it as $2 = 1.11 = 1 + \phi^{-1} + \phi^{-2}$ we can take the $1$ for $x$ leaving $y = 0.11 = 1.00 = 1$ for $y$, which simply recovers $x = 1$ and $y = 1$.
$\sqrt 5$ is already directly representable in base-$\phi$, but if we wanted to use integers, $x = 2$ and $y = 1$ works just fine, and base-$\phi$ for $5$ doesn't give us a better convergence.
Now for the fun part.
$5 + \sqrt 5 = 10000.01 = \phi^4 + \phi^{-2}$, so $x = \phi^2$ and $y = \phi^{-2}$ will give good convergence, and
$5 - \sqrt 5 = 100.0001 = \phi^2 + \phi^{-4}$, so $x = \phi$ and $y = \phi^{-4}$ will give good convergence, both in a finitely representable periodic form.
Combinations of these factors like $\sqrt 6 = \sqrt 2\sqrt 3$ (for $15^\circ$) and $\sqrt 2\sqrt{5 + \sqrt 5}$ (for $12^\circ$) are also periodic GCF's.
This gives us a nice finite way to represent vectors made from sines and cosines of integer multiples of $3^\circ$.
So to answer my original questions:
- Yes. One problem is that uniqueness is lost for CF representations. There are infinitely many ways to represent the same CF. This is related to the problem base-$\phi$ has in that there are infinitely many finite ways to represent the same number (using the 100 = 011 conversion). This is not a problem as long as we can find a consistent representation for numbers we are interested in.
- Yes, at the cost of uniqueness.
- One advantage is potentially faster convergence of a GCF than with only integers. Another is the ability to represent quadratic extensions (square roots) of $\mathbb Z[\phi]$ in a periodic form.