I've never thought of Toads as being actual mushrooms; they're mushroom people. It does seem that they do have some mushroom-like qualities other than physical appearance. I can specifically think of M&LPiT (don't want to spoil, though), although I can't think of anything else specific off the top of my head (hehe).
Their diet seems to consist mostly of mushrooms, but sweets seem to be really up there, too (syrups, cakes, cookies, etc.). I also vaguely remember them eating meat of some sort (GASP! They're omnivores!!); unfortunately, I can't remember what, exactly. I think it was either in PM2 or M&L2.
Yoshis mostly eat fruit, although I remember Toads eating fruit as well. Plants, vegatables, and nuts, too.
I also tend to think of it this way: in M&LSS, the dominant species were Beanbeans---humanoid beans--and their diet seems to consist mostly of beans. The "evolved" humanoid-hybrid species seem to eat their "devolved" counterparts. I would not call it cannibalism; the people are complex humanoids, while what they eat is simplistic.
NE said it very well.
As for the Toad/Yoshi thing, think of it this way: there are guys named "Guy".
Edit: Oh yeah, I was also going to comment on the Peach/Bowser thing. Peach has magical powers, yes, but so does Bowser. While she can fight up to a point, Bowser--not to mention Magikoopas and others that have magical abilities--can overwhelm her with their physical strength, as well.
Also, she's usually taken by surprise; when that happens, I imagine it's hard to quickly defend herself. Not to mention, if she can take one out, there's usually a whole gang of enemies, too. She's outnumbered.
In SSBM, I noticed that while she's extremely good at fighting, of all the fighters, Bowser seems to be able to toss her around the best; she's very agile and had great come-back abilities when thrown off-stage, but she's very light and Bowser is really powerful. Her agility makes up for the physical strength, but when taken off-guard....well, you get the idea by now.
