Weight loss is never purely fat. Some proportion of what comes off is lean tissue — muscle, organ mass, bone. That's true of any deficit, however you create it.
What's specific to GLP-1s is the speed and the appetite suppression. Losing quickly, while eating considerably less than usual and often without particularly trying, is the combination most likely to take muscle along with the fat. Trial data on these compounds has consistently shown a meaningful share of total loss coming from lean mass.
Two things change that, and neither is complicated.
Protein
A higher intake gives your body a reason to keep muscle rather than break it down for fuel. This is why the calculator sets 2.2 g per kg when the GLP-1 box is ticked, rather than the 1.6 g it would use otherwise.
Resistance training
Protein gives the material; training gives the signal. Two or three sessions a week is enough to change the outcome substantially. It doesn't need to be complicated or heavy.
Not eating less
The instinct on a GLP-1 is to lean into the reduced appetite. But the deficit is already there — pushing it further mostly costs you muscle rather than buying faster fat loss.