I expect it's been answered (but not in the first few). In the menus find "preview WB/Exposure in manual mode" turn it off.
Same on all Fujis. should have been off by default on a new camera.
Vic
--
The sky is full of holes that let the rain get in, the holes are very small - that's why the rain is thin.
Spike Milligan. Writer, comedian, poet, Goon. 1918 - 2002
Unfortunately for the OP, who wants to have manual focusing at maximum aperture for narrowest DOF and pinpoint accuracy at all times, whatever the selected aperture is, the X-T100 behaves differently to all the other Fujis. It's mind-bendingly complex, given all the potential variables, so I wrote down some observations comparing the X-T100 and X-T20 behaviours side by side, with the same lens fitted (15-45 PZ XC, since that's the only lens I have two examples of), following the types of scenario the OP and advent1sam have mentioned. Anybody who wants to ask what happens at other settings/other exposure modes etc., please ask!
So...
Manual exposure mode, Auto ISO, manual focus, magnification on (or off, it doesn't actually seem to alter the behaviour), f5.6, 1/8 sec in bright sunlight (so obviously, a severely overexposed shot will result):
X-T20, WB/Exp preview in manual set to ON - aperture stays at f5.6, live view appropriately whited-out.
X-T100, Exp preview in manual set to ON - the same as the X-T20.
X-T20, WB/Exp preview in manual set to OFF - aperture stays at f5.6, live view simulates a normal exposure for comfortable viewing only, presumably achieved electronically on the sensor. So, the aperture behaviour is the same as the two examples above - it stays wide open.
X-T100, Exp preview in manual set to OFF - aperture stops down varying amounts according to the precise aiming (including down to values like f16 by the looks of it) to achieve a normal exposure on the live view image. So in this case, the X-T100's behaviour is completely different to the previous three examples.
Next, I kept all the settings the same (manual focus, manual exposure, auto ISO, f5.6, magnification on) but set a shutter speed of 1/160.
X-T20 with WB/Exp preview in manual set ON - as before, the aperture stays wide open, and the live view shows the milder overexposure of this setting.
X-T100 with Exp preview in manual set ON - the aperture stops down a little (unexpected!) - presumably it's using this to lessen the amount of overexposure shown in live view to an appropriate amount.
X-T20 with WB/Exp preview set to OFF - again, the aperture stays wide open, and the camera simulates correct exposure for comfortable viewing, rather than the actual mild overexposure that will occur in the shot.
X-T100 with Exp preview set to OFF - the aperture dynamically varies and stops down a lot when it feels the need, to enable it to show a correct exposure for live view comfort which will of course not be delivered on the actual, mildly-overexposed shot.
In all cases above, the view is either magnified or not for manual focus (doesn't seem to alter the behaviour) and no half-pressure is applied to the shutter release.
Summary of the above - the X-T100 uses its aperture mechanism to control the appearance of live view when in manual exposure, manual focus mode, stopping down to a greater or lesser extent as it feels the need, even when the aperture is set to wide open for shooting. The X-T20 keeps the aperture at f5.6 in all instances in these scenarios.