Template Stacking and Statistics

[Grindle]

Can the order in which templates are applied ever result in multiple creatures with different stats, but the same templates?

[Devmaar]

Yes, for example Feral and Mineral Warrior both apply Int penalties, but to different minimums.

[Phelix-Mu]

Beyond ability scores, the answer is an even bigger yes, because there is variation in what different templates allow you to keep from your earlier types/traits/special attacks/special qualities, and so forth. If the final template removes a bunch of stuff granted by earlier templates, this can lead to a decidedly sub-optimal result.

Some templates also give non-abilities, such as Con-- and Int--. It is possibly to have such a stat at one point and then get it back at some different quantity than originally present (awaken undead is the only method jumping to mind, but I'm sure there is some other way out there), then a further acquired template to change it further.

[Snowbluff]

Yes, for example Feral and Mineral Warrior both apply Int penalties, but to different minimums.

This a bad example, since Feral is inherited, and Mineral Warrior is not. Since you would get mineral warrior later, you would use its worse Int minimum, IIUC.