The OED recognizes three definitions of milestone--the original marker on a road, a marker of progress, and the sense adopted in U.S. program planning (the only one where I quoted the first instance, to show that this is a more recent use).
milestone, n. and adj. A. n.
a. A stone or (usually short) pillar set up beside a road indicating >the distance in miles from that point to a particular
place.The reference in quot. lOE may be to a Roman milestone on a
road in England.
b. fig. A significant stage or event in the progress or development of a society, a career, an individual's physical and
mental growth, etc.; a measure of progress or change. Cf. landmark n.
c. fig. orig. U.S. A stage to be reached (in a project, etc.), esp. by a specified date; a target.
1958 PERT Summary Rep. Phase 1 (Bureau of Naval Weapons, U.S. Navy)
2/1 The progress information is based upon a sequence of important
milestones together with their scheduled dates for accomplishment.
So an Eagle Scout badge would be, to me, an accomplishment (I didn't look it up in the OED). Milestones can be accomplishments. The words clearly overlap. A project might be working on something, e.g., development of an application.