You’re generally right, however threshold crossing height is not the same at every airport, with regard to both the VGSI and the electronic glideslope. And many VGSI and GS aren’t even harmonized/coincident (which is usually noted in the approach chart). So speaking of a specific TCH in a global way (without specifying a particular airport/runway) is going to lead to false expectations.
However, at procedurally-generated airports, VGSI always default to a certain distance beyond the threshold, which further skews the TCH. Long and short - they aren’t always installed in the same location and that affects TCH. In this, the sim is incorrect in a very broad manner and you’re correct.
Bug report thread about it here.
The only way to fix it in the base sim that I know of is to use the World Hub, which we’re still awaiting.