well the words themselves are different..
I dont know what arnis means but kali = weapon and escrima = stick
like you said, my guess would probably be that the differences came from what people decided to focus on.
Maybe escrima focused more on the use of the stick while kali looked at all of the weapons they used.

the techniques are essentially the same, but sometimes taught differently. Like body positioning for a certain strike might be different depending on who you're learning from.
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"you're going to work till you wish you were dead and then keep going.." -Sgt Slaughter