Understanding modification in place

If I run it from the command line, I get:

Global
@1050bb840 13 INTSXP g0c2 [MARK,NAM(1)] (len=3, tl=0) 1,2,3
@1050bb840 13 INTSXP g0c2 [MARK,NAM(1)] (len=3, tl=0) 1,1,3
In function
@1050bb190 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,2,3
@1050bb190 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,1,3

i.e. both modifications occur in place.

If I put it in a file and source() it, I get:

Global
@1050bb318 13 INTSXP g0c2 [NAM(2)] (len=3, tl=0) 1,2,3
@1050bb698 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,1,3
In function
@1050b8958 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,2,3
@1050b8958 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,1,3

i.e. in the global environment a copy is created.

Why is there a difference?

Did you look at source()? ;)
It has to do with all the additional processing there which assigns the result of every line locally thus producing extra copies. If you just eval it, you'll get the same behavior as in the console: