The difference between activating them is important if you want to use gelatin instead of agar. Gelatin is made of proteins and peptides and agar is a polysaccharide.
Gelatin should not be boiled, because it breaks down. Agar needs 95 deg C to dissolve, so usually it is simply boiled. This means, that if your receipe calls for boiling the agar with stuff you want to gel (e.g. fruit), you have to add gelatin later, when all the boiling is finished, but the mixture is still hot enough to dissolve the gelatin.
Also, agar will work on some fruit, that prevent gelatin from geling, like pineapple or kiwi. If you want to use these fruit with gelatin, you have to boil them (or so they say - I have access to agar, so I never tried gelling boiled pineapple with gelatin).