Also consider the width of the rim. You've got two different ones there, I'll bet they are not the same width where the tire mounts, so that can cause some variation on ho the tire sits on it. Biggest issues are trying to use tires that are small or too large for your rims - both can cause problems. If it looks like the tires are seating properly on the rims (it appears both are in your photos) I wouldn't worry about them if the ride is comfortable.

And yes, I've seen variations where one manufacturer's 28mm tire is as big as another manufacturer's 25mm tire (both worked fine). Me, I use 28s or 32s on my bicycles (35s on my tourer), mainly for the comfort vs a 23mm tire.