I contacted my foundry (over e-mail and phone).
They said:
1) They use stencils of four heights: 80 um, 100 um, 127 um and 150 um. Standard (typical) stencil is of 127 um height.
2) Height of solder paste after application of a stencil (before heating) cannot be greater than height of stencil.
My comment: I don't remember for sure, but I think they meant, that average height of solder paste is equal (not just not greater) to height of stencil.
3) After heating (reflow) component descends.
So, I conclude:
The height of component after reflow soldering is smaller than nominal (datasheet) component's height plus height of stencil. Or, in other words, the ceiling value for component's height after reflow soldering is component's nominal height before soldering + stencil height.
PS1: I looked at several hand soldered capacitors. I do agree (with comments to the question) that the increase in case of hand soldering is uncontrollable. The additional height due to relatively large solder fillets under and above capacitors was as much as 0.5-0.6 mm (measured with eye).
PS2: Unfortunately, I don't have any reliable estimates how much the component descends after heating.
PS3: As soon as the PCB is produced and components are reflow mounted, I plan to update here about the resulting height and the socket.
Short: Try rotating the controller 180° before soldering :)
Long: The ST controllers have two marks on the top side, only one is for Pin 1. And most times you choose the wrong one.
The rotation will connect some GND and VCC pins so you get a short circuit.
To identify the right "Pin 1" you could have a look at the chip datasheet in the section Package Information / Device Marking.
( If you could read the text on the chip, pin 1 is in the lower left corner)
Best Answer
No, this is generally not possible because of the rest of the circuit. If you have a schematic you may be able to analyze the circuit and figure out what the value is from the 'incorrect' reading, but that is not always possible, even under ideal conditions. By ideal, I mean that you have a perfect understanding of the circuit, how you measuring instruments work (for example the waveforms used to measure capacitance including the voltages on each range) and how parts such as the chips Nick mentions behave when not powered and subjected to those waveforms). If a much smaller and/or less accurate part is effectively in parallel it may be impossible to get an accurate number.
The most reliable way is to remove the parts with a tweezer type desoldering tool and measure it, then replace. Some larger (0603 and up) resistors are still marked but there are many smaller resistors and most SMT capacitors that are not marked at all (photo from here).