I agree this is annoying behavior! (RStudio also has Control-A and Control-E mapped to "Go to beginning/end of line" by default, and the same thing occurs). If you want to suggest this as a feature request, here's the guide for how to do so: https://github.com/rstudio/rstudio/wiki/Writing-Good-Feature-Requests
The current behavior seems to interact with soft-wrapping — in situations where the editor contents are soft-wrapped, "Go to beginning/end of line" actually goes to the previous/next wrap point. When you have soft-wrapping turned off, it does properly go to the beginning/end of the line (as indicated by the line numbers). I can understand the logic behind making the "end" of the line the wrap point when lines are soft-wrapped, but I find it is rarely what I actually want to do. FWIW, the MacOS shortcuts are officially described as "Move to the beginning/end of a line or paragraph".
Examples:
R script, no soft-wrapping
Control-E goes to end of line:

R script, soft-wrapping turned on in Global Options
Control-E goes to end of wrapped line (but see cursor position box in lower left: not actually the end of the line)

Text file, always soft-wraps
Control-E goes to end of wrapped line (but see cursor position box in lower left: not actually the end of the line)
