According to your second paper,
The two-doublet structure gives rise to five physical Higgs bosons via spontaneous symmetry breaking; two neutral CP-even particles h and H with mh ≤ mH , one neutral CP-odd particle A, and two charged Higgs bosons H±. In these models the ratio of the vacuum expectation values of the two Higgs doublets, tan β, and the mixing angle between h and H, α, are important free parameters. These can be tuned to the alignment limit sin(β − α) = 1 whereby h aligns with the properties of the SM Higgs boson, while the additional Higgs bosons may appear at TeV scale or below it.
I think the way to interpret this paragraph is that the combined phase $\beta-\alpha$ is ”aligned” to make the proposed new particle “orthogonal” to the observed Higgs, which appears to be consistent with the Standard Model.
I don’t know enough about the physics here to know whether the sign of $\beta-\alpha$, whether the new field is “clockwise orthogonal” or “counterclockwise orthogonal,” is a physically meaningful question or not.
Your first reference does discuss the “wrong-sign Yukawa” limit $\sin(\beta+\alpha)=1$ and values for $\tan\beta$, which suggest that the angles $\alpha,\beta$ are constrained separately.
In your first reference, Figure 5 is an “exclusion plot” with $\cos(\beta-\alpha)$ as a parameter. For this purpose, the $\cos \approx 0$ region is clearly superior to the $\sin \approx 1$ region. The trig functions are monotonic near their zero crossings, but have rising and falling regions near their maxima or minima. Consider the transformation
\begin{align}
x & := \frac\pi2 - (\beta-\alpha) & |x| &\lesssim 1
\\
\cos(\beta-\alpha) = \sin x &\approx x - \frac{x^3}{3!} \approx x
\\
\sin(\beta-\alpha) = \cos (-x) &\approx 1 - \frac{x^2}{2!}
\end{align}
If we have reason to believe that some phase $\phi$ is approximately a quarter-turn, looking at $\cos\phi\approx 0$ lets us determine $\phi$ uniquely. Meanwhile, some value $1 \neq \sin\phi\approx 1$ corresponds to two possible angles. In addition to the ambiguity, the small-squared dependence on angle also costs precision. Linear approximations are easier to deal with than quadratic approximations.