This might not be an answer, but is too long for a comment.
Assuming $t_0<t_f\land \epsilon>0$, the Mathematica Integrate function gives the result
$$\int\limits_{t_0}^{t_f} \tanh\left(\frac{x}{\epsilon}\right)\, e^{-i \omega x} \, dx=\frac{\omega \epsilon e^{-\frac{1}{2} \pi \omega \epsilon} \left(B_{-e^{\frac{2 t_0}{\epsilon}}}\left(-\frac{1}{2} i \epsilon \omega ,0\right)-B_{-e^{\frac{2 t_f}{\epsilon}}}\left(-\frac{1}{2} i \epsilon \omega ,0\right)\right)-i e^{-i t_0 \omega}+i e^{-i t_f \omega}}{\omega}\tag{1}$$
whereas the Mathematica FourierTransform function gives the result
$$\mathcal{F}_x\left[\tanh\left(\frac{x}{\epsilon}\right)\, \left(\theta\left(x-t_0\right)-\theta\left(x-t_f\right)\right)\right](\omega)=\frac{1}{2} \epsilon e^{-\frac{1}{2} \pi \omega \epsilon} \left(B_{-e^{\frac{2 t_0}{\epsilon}}}\left(1-\frac{i \epsilon \omega}{2},0\right)+B_{-e^{\frac{2 t_0}{\epsilon}}}\left(-\frac{1}{2} i \epsilon \omega ,0\right)-B_{-e^{\frac{2 t_f}{\epsilon}}}\left(1-\frac{i \epsilon \omega}{2},0\right)-B_{-e^{\frac{2 t_f}{\epsilon}}}\left(-\frac{1}{2} i \epsilon \omega ,0\right)\right)\tag{2}$$
where $\theta(x)$ is the Heaviside step function and $B_z(a,b)$ is the incomplete beta function.
The Fourier transform result in formula (2) above was evaluated using FourierParameters$\to\{1, -1\}$ which is equivalent to $a=1$ and $b=-1$ in formula (15) at Wolfram MathWorld: Fourier Transform, and consequently the Fourier transform result above should be equivalent to
$$\int\limits_{=\infty}^{\infty} \tanh\left(\frac{x}{\epsilon}\right)\, \left(\theta\left(x-t_0\right)-\theta\left(x-t_f\right)\right)\, e^{-i \omega x} \, dx=\int\limits_{t_0}^{t_f} \tanh\left(\frac{x}{\epsilon}\right)\, e^{-i \omega x} \, dx$$
and so the results in formulas (1) and (2) above should be equivalent, but I haven't confirmed their equivalence.