I stumbled upon the definition of equivalent compactifications which is:
Two compactifications $Z_1$ and $Z_2$ of the space $X$, are said to be equivalent if there exists a homeomorphism $h:Z_1\rightarrow Z_2$ such that $h(x)=x$ for every $x$ in $X$.
I find it interesting that this definition includes the "$h(x)=x$ for every $x$ in $X$" part as it seems to me very weird to be able to compactify a space $X$ in two different ways, have them be homeomorphic, but have no homeomorphism that fixes every point of $X$. I however know very few examples of compactifications which might explain why I can't produce a counterexample to this.
My question is: Can you give me an example of a space $X$ and two compactifications of $X$ such that they are homeomorphic but not equivalent?
P.S. The book that I'm reading (Munkres) includes Hausdorff in its definition of compactification, which I don't know if it is usual or important here. It goes: If $Y$ is a compact Hausdorff space and $X$ is a proper subspace of $Y$ whose closure equals $Y$, then $Y$ is said to be a compactification of $X$.
Since compactifications also depend on how the embedding is done, we can cheat a little bit (or a lot). Consider the space $X = (0,1) \times \{ 0, 1 \}$; that is, two disjoint copies of the open unit interval.
Two inequivalent but homeomorphic compactifications of $X$ are $$\begin{align} Z_1 &= ( S^1 \times \{ 0 \} ) \cup ( [0,1] \times \{ 1 \} ), \\ Z_2 &= ( [0,1] \times \{ 0 \} ) \cup ( S^1 \times \{ 1 \} ). \end{align}$$ where $S^1$ is the one-point compactification of $(0,1)$, aka the unit circle.
For an example using the stronger form of equivlanece from David C. Ullrich's answer, take the original space to be $$X = ( (0,1) \times \{ 0 \} ) \cup ( ( ( 0,1) \cap \mathbb Q ) \times \{ 1 \} )$$ (only use the rationals in the second copy), but the same compactifications $Z_1,Z_2$ as above.