Say that an algebra $\mathfrak{A}$ (in the sense of universal algebra) is point-transitive iff for every $a,b\in\mathfrak{A}$ there is a $\pi\in Aut(\mathfrak{A})$ with $\pi(a)=b$. While genuinely point-transitive algebras are somewhat rare, many naturally-occurring algebras yield the same clone as a point-transitive algebra. Specifically, given an algebra $\mathfrak{A}$ let $\mathsf{Cl}(\mathfrak{A})$ be the smallest set of functions from some finite Cartesian power of $\mathfrak{A}$ to $\mathfrak{A}$ which contains all the constant functions and projection functions, all the primitive functions of $\mathfrak{A}$ itself, and is closed under composition. (EDIT: as Keith Kearnes states below, this is actually the polynomial clone of $\mathfrak{A}$.) Then:
Each group $(G;*,{}^{-1},e)$ yields the same clone as its "torsor reduct" $(G;(a,b,c)\mapsto a*(b^{-1}*c))$, which is clearly point-transitive since each $x\mapsto y*x$ is an automorphism.
A similar trick works with rings: each ring $(R;0,1,+,-,\times)$ yields the same clone as $(R; (a,b,c,d,e)\mapsto (a-b)(c-d)+e)$, and the latter is again point-transitive via maps of the form $x\mapsto x+y$. (This is basically due to Matt F.)
Say that an algebra $\mathfrak{A}$ is almost-point-transitive iff we have $\mathsf{Cl}(\mathfrak{A})=\mathsf{Cl}(\mathfrak{B})$ for some point-transitive algebra $\mathfrak{B}$ with the same underlying set. I'd like to just ask "Which algebras are almost-point-transitive?," but I don't see how to make that precise in the right way (e.g. to avoid "the almost-point-transitive ones" as an answer). Instead, the following seems like it might be more immediately approachable:
If $\mathfrak{A}$ is almost-point-transitive and $\mathfrak{B}\in\mathsf{HSP}(\mathfrak{A})$, must $\mathfrak{B}$ be almost-point-transitive as well?
I strongly suspect that the answer is negative but I don't see how to construct a counterexample.