It makes them homogeneous in what they are. It makes the whole thing more realistic/believable. At least they are all physical object. A shard is a piece of glass. A creature shard (or spell in a lesser way) is somehow ridiculous. It is IMO as ridiculous a having an elf being a spell, a necklace being a creature or an incantation being a permanent.
From a thematic standpoint, I'd always assumed the spell-shards were physical objects where you threw the shard and then X happened and expelled its magic and then the shard was just a little piece of worthless crystal on the ground (think the original unupped shards). I also assumed SoI was a spell that made a golem rise up out of the ground with little pieces of crystal sticking out of it.
Can't explain SoFo.
edit: To continue my theme assumptions, the permanent-shards were little crystals that
didn't expel their magic immediately when you tossed them, and instead kept putting their energy out. Also, lol at all the people who don't see "magic jewels" as a common trope in fantasy settings.
edit2: For that matter, magic crystals are a common trope in RL settings, at least if you're ever around hippies.