That is indeed a very strange behaviour. I can see what you are describing and probably @GreenSock is the individual that will be able to tell you why exactly this is happening and if there's anything he can do about it.
I can only have a guess based on inspecting the element and what I know of SVG behaviour. Basically, everything is doing what is supposed to do, in my eyes. The catch is how stroke-dashoffset and stroke-dasharray work together with the length of the line you're working with. I will assume you know the theory behind animating a stroke in SVG (if you don't, let me know and I'll dig something out from the interwebs).
All is working wonderfully until you rotate the line - as soon as you do that, it looks like the line is no longer the same length and Safari is not having a good time working out where the visible bits of the stroke should be. When inspecting the line, you will see that it is in the right place and the correct length but, the stroke-dashoffset is not quite where it should. Possibly a Safari bug... Possibly something @GreenSock can fix with his magic. Possibly, that's something you need to take in consideration when creating your SVGs...
I've amended my pen to just rotate one of the lines, so you can compare them.
PS: As for the selector engine - The difference will probably be negligible unless you are selecting thousands of elements - even then, it's probably not worth fretting over it. I never use jQuery myself - don't really need it - so I default to GSAP's selector. Less code to write.