The rational canonical form of a matrix is almost never a diagonal matrix. A typical rational canonical form is a companion matrix:
$$\begin{pmatrix}0&0&0&\cdots&0&-a_0\\1&0&0&\cdots&0&-a_1\\ 0&1&0&\cdots&0&-a_2\\ \vdots&\vdots&\vdots&\ddots&\vdots&\vdots\\ 0&0&0&\cdots&0&-a_{n-2}\\ 0&0&0&\cdots&1&-a_{n-1}\end{pmatrix}$$
Even if the roots are all distinct and the matrix is diagonalizable, that's the form we'll choose to call the rational canonical form. When the RCF isn't of this form, it's because the minimal polynomial has lower degree than the characteristic polynomial - and then we build the RCF using companion matrix blocks. These companion matrices have integer entries when the associated polynomials have integer coefficients, which is certainly true for the minimal and characteristic polynomials of integer matrices.
In fact, the only way for the RCF to be diagonal is if the matrix is a multiple of the identity. In that case, there's no way for it to be similar to anything else.