Even building the appropriate structure on the bonus tile, however, does not result in obvious effects. E.g., if I build a basic factory on a 100% manufacturing bonus tile, the main planet screen shows that tile as producing, IIRC, 8 mp, just like all the other basic factories that are built on ordinary tiles. If I go to the summary screen in the planet viewer, all of the basic factories are listed as producing exactly 8 mp, despite the fact that one should clearly produce 16 mp. Most significantly, at the bottom of the summary screen, where it provides the totals of all the benefits the structures on the planet provide, the total does not appear to reflect a 100% bonus to one of the manufacturing tiles (once you account for the mp provided by the Initial Colony).

Now, I'm willing to assume that the bonuses are actually being applied. But it sure doesn't LOOK like they're being applied. I've noticed this for manufacturing bonuses and morale bonuses. I haven't had the chance to check research or food bonuses, however. If the bonus is being applied, it might be helpful to have some indication of that, at least in the planet summary screen.

Yup, that is correct.
The tile bonuses are being applied in spite of the fact that you cannot visually see this in the details section when the building on the tile is selected -or- in the summary screen.
You can verify this by playing around with your spending and running the numbers yourself.
The only place the bonus will show up is in the resultant production numbers at the top of the screen. Those are being calculated with the bonuses.
I'm not necessarily sure I agree that the building details when you click on the tile should reflect the bonus, since you're really looking at the building details, and not the complete picture including the tile you know? There's something to be said for knowing that you have a 10mp factory on the tile, and not a 12 mp one, regardless of the overall output due to the bonuses. I could go either way on that.
But I certainly agree that the summary screen ought to reflect the bonus. Those combined total production limits at the bottom ought to be accurate, and right now they really aren't.