My answer might be biased, so I hope someone else could complement it adding different viewpoints. Moreover, my answer is essentially philosophical, so it might sound incomplete in case you are searching for a technical answer.
I can underscore two threads in answering your question:
SDG and "Differential Geometry over general base field" are extremely flexible in creating the type of nilpotent infinitesimals you need for your problem. This is essentially because they are algebraic in nature. Like for Weil functors, these theories are wonderful generalizations of the same basic idea of the ring of dual numbers $\mathbb{R}[h]/(h^2=0)$. We can summarize this point of view, even too strongly, citing J. Conway who in The Math Forum Drexel of Feb. 17, 1999 said "SDG is just a formal algebraic technique for 'working up to any given order in some small variable $s$' - for instance if you want to work up to second order in $s$, you just declare that $s^3 = 0$".
In my opinion, it is really difficult, or even impossible, to achieve the same formal power and beauty in other theories of nilpotent infinitesimals.
On the other hand, Fermat reals are formally less powerful, but strongly intuitively clearer. This permits to gain intuition about possible developments of the theory of nilpotent infinitesimals which seem impossible following an algebraic approach. So, in the ring of Fermat reals, one can define a meaningful notion of $n$-th root of a nilpotent infinitesimal, with application to fractional calculus, there is a computer implementation of the whole ring, and we are working to define reciprocal of nilpotent infinitesimals and also stochastic nilpotent infinitesimals corresponding to Ito's calculus. This teaches us many things about nilpotent infinitesimals. If you want to write new papers (frequently simply reformulating SDG!), Fermat reals is the right framework. Therefore, the first thread to compare these theories could be: do you prefer more formal power but a lacking intuition or less formal power but a greater intuition?
The second thread can be summarized with the question: with whom do you want to talk? Very few people have a so strong formal control of the mathematics they are doing to have a sufficient sure sense that they are correctly working in intuitionistic logic. More generally, in my experience, for some mathematicians, a strong intuition is essential to like a theory. For this reason they found difficult to work in SDG or in a purely algebraic "formal" approach. Fermat reals have not this problem and are frequently well accepted by analysts, geometers and physicists.