stuff and nonsense
im not really awake so i may be wrong or imprecise here, but given a linear transofrmation T, on a space V, i.e. from V to V, finite imensional, there is a minimal polynomial p such that p(T) is identically zero on V.
the short answer to your question is that both procedures you describe yield the minimal polynomial for the lienar transformation D (i.e. differentiation), on the space V of solutions of that differential equation.
I.e. the original de may be viewed as giving the minimal polynomial P(D) and asking for the largest space of functions on which it is the minimal polynomial.
On the other hand, suppose P has degree d and V has dimension d and P(x) is the minimal polynomial of D on V. Then there isa theorem that there is a "cyclic" basis for D on V, and in that basis the matrix for D is a companion matrix A for that polynomial.
Hence the minimalpolynomial P, can be calculated as the characteristic polynomial, i.e. det(X-A).
as for plugging in e^(xt) for y in the original equation and geting P(x) = 0, that is kind of an ad hoc way of just substituting x for y in the equation and powers for derivatives, i.e. of writing the equation as P(D).
It is a little misleading since it suggests that all solutions of the equation hVE FORM e^ct, which they do only if the roots are distinct.
A better way of doing it is to look at the equation as P(D) = 0, and factoring the equation as a product of powers of (D-c) for vaRIOUS C'S, not necessarily all different. i.e. a product of powers (D-c)^s for different c's.
Then solving the equation is the same as solving each of the equations
(D-c)^s = 0, which shows where the additional solutions come from that are not of form e^(ct).
This amkes it look more like a jordan form approach, and now one sees perhaps that another answer to your i=uestion is that one calculation computes the minimalpolynomial from the jordan matrix and the other computes it from the companion matrix, and they give the same answer.
i have equated mnimal and characteristic polynomials in this discussion since in this case they agree. i.e. the dimension of the null space of (D-c)^s is always s for this operator D.
But on some spaces, and with some other operators, the null space, of T-c could be more than one. that is when the characfteristic polynomial is bigger than the nimal one, but this do3s not sem to happemn for the deriavtive operator D, since Dy = 0 always ahs one dimensional solution (on an interval).
