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the difference between Javacard and GlobalPlatform is the same as the one between a falcon and a carrot.
yeah, you can't compare.
javacard is about executing applets on anything that can exchange apdus. It does not care about how to put an applet somewhere. it can be anything, provided that you implement what the jc spec says.
GP is about loading applications in things that can exchange apdus. It does not care about javacards. It can be any application, and it officially works with multos, but it could be anything, provided that you implement what the gp spec says.
The confusion is that in mostly all cards, these two "sleep together" (french expression, sorry :) ) because they were both invented and promoted by the same consortium (visa open platform), that later separated and evolved into jc 2.x.x and gp.
And there are very little other combinations (gp multos cards are said to exist, I never saw one, and that's all). At a moment the gp spec contained a microsoft dot net card API, but it disappeared in gp 2.2.
apdutool is an ad-hoc tool made by sun to start an applet in the sun javacard simulator (iirc) so it compares to global platform, but is not compatible with it. They made it as simple as possible, this is a "bare minimum" loader.
No real card is compatible with apdutool commands, they all implement GP.
On the contrary I'm not aware of any public javacard simulator that implements GP.