@KernalCrush, Academically, you're right. Different sugars refract differently. Its physics.
What's measurable is relative changes, rather than absolute sugars. We base those relative measurements on distilled water as a 0.00 baseline. I don't want to be contentious, so what follows is just some of my thoughts and experience. I appreciate that you want to understand the difference.
In your example, did you boil the DME to remove proteins? If not, those were suspended in the solution and showed up in your reading.
Even if you did boil to coagulate proteins, there are still some left in suspension, along with trisaccharides, polysaccharides, tannins and a host of other malt components that make the difference between beers' residual post fermentation gravity and the 0.990 reading of fermented sugar and honey (grapes, too). All that crap changes refraction, too.
Table sugar and honey will have a far higher percentage of a "pure" sugar to measure. Sucrose is somewhat easy to purify, which is why it's the standard. Do the same test with a "raw" or brown sugar and I suspect your results will vary a bit.
In my previous example, I was pointing out that different sugars also refract various light wavelengths differently. So, a mixed solution can be teased apart and analyzed. This is waaaaay beyond the needs of homebrewers and all but the most "engineered" of breweries.
BeerSmith's gravity number is derived from malt analysis numbers. These are measurements of absolute levels of dissolvable solids (aka 100% efficient extract), which include things you don't want in your beer, like tannins. This is going to read higher pre-boil than post, if you were to add back the water from evaporation. BeerSmith calculates each grain or sugar source individually when predicting a reading.
The most practical example I can give you is my post boil and post chill numbers. With an all malt wort. Post boil, I might have a reading of 17 Plato. Post chill, the reading falls to ~16.8 and change. The difference? Cold break is still suspended in the post boil number, but has coagulated out in the post chill number, causing it to be lower.