At 1:1, both a 50mm and a 100mm macro reproduce the subject at life size on the sensor. The difference is not magnification, but how far the lens can be from the subject to achieve that magnification.

In general, a longer macro lens gives more working distance than a shorter one at the same 1:1 ratio, which is why longer macros are often preferred for insects and other easily disturbed subjects. However, working distance is not determined by focal length alone. It also depends on the lens’s optical design, including where its nodal points are and how the lens focuses internally.

So yes, there is a real difference between 50mm and 100mm macros at 1:1, but it may be smaller than expected with some lens designs. A 100mm macro usually lets you stay farther back than a 50mm macro, but “farther back” in true macro terms can still feel quite close. Your observed front-of-lens distance can also be much shorter than the lens’s stated focus distance, because focus distance is measured from the sensor plane, not the front of the lens.