If two things are entirely different, that means there are absolutely no common properties. If they are mostly different, they may have a few properties in common, but the majority of their properties are different. It is entirely clear that the two sentences are at most somewhat different. Whether or not there are any differences in meaning depend on what you mean by "meaning". Your best hope to maximize differences in meaning is to include pragmatic / usage differences (appropriate, if the framework is cognitive linguistics). But these are extremely unnatural constructions, the type only constructed by linguists. The only animals that might have hands are apes (they aren't called "hands" on dogs, cows or raccoons). Three is the wrong number: therefore you would have to say "only three", since you're describing an unnatural state. If you meant "three fingers on each hand", you'd say "only has thee fingers on either hand". Otherwise, you'd say something like "only has a total of three fingers". However, there is also the hyena scenario, where you could say "this hyena has 3 fingers, and that hyena got the rest" (you can fill in the gaps). In other words, pragmatically speaking, you can't compute "meaning" with zero context, thus you have to either specify a context, or you have to say "in any imaginable context".
In the latter case, you have to consider the possibility of animals that have fingers on their hands and on their bellies, so these quasi-Moties have a total of 9 fingers, 3 on their one hand and 6 on their belly. In that case, sentence 1 is true and sentence 2 is false.
