Regardless of tolerance 99% is going to be twice as powerful as 50% (Of course it can be extremely hard to tell with Crystal since for example shake and bake or 1 pot, can then be crystallized though its almost NEVER as potent as say Birch or P2P cooks) So just cause you have a shiny shard, only says so much.
Being said though Crystal is almost ALWAYS more potent because the "cook" would need experience to finalize the MA into a crystalline form. Well at least a good bit more than it takes to read a page on the web and make shake and bake.
Also I don't see how the acidity level comes into play in most situations since you need specific basify correctly your product to make it "usable".
Sodium chloride will make the same shape of crystal no matter what ocean you got it from, or if you re-crystallized it in your kitchen. You would need some serious equipment to identify trace halogen isotopes to tell different crystals apart.
Now there is all that colored salt out there, and types of course salt, but if you look closely, you'l see that they are NOT perfect little crystal cubes (iodide is almost the same size, properties as chloride)
Same with meth: a crystal will be a crystal. And, a racemic mix will form a different type of crystal than either isomer, no matter how you prep it. The bad meth cook would just never get a visible crystal--he'd get some powder, maybe some tiny shards.
What sort of pH adjustment that may or may not happen, depends on how it was made. A solid object has no final pH, which is only defined for solutions in water. The pH adjustment might have occured as a purification, or to promote one form of product over another.
"Usable" product and pH: you have either the acid salt as a pure solid, or the free base. The base form would have no charge, so it's solubility in water goes toward zero, and you wind up with a flammable liquid at room temp, bad for transport.
