I'm sure there have been times when dies were deliberately marked, but it's not a general thing.
In the early years, all dies were handmade and no two were exactly the same, so the markers start by relating to the slightly different positioning and structures of the design elements.
Mintmarks were hand punched into US dies until 1990 - for small population coins (such as the 1909S VDB
Lincoln Cent), there are only four obverse dies used and checking those markers is an important part of verifying a coin. If the S doesn't match one of the four specific known positions, it's fake.
Today dies are created from computer-aided manufacturing and - theoretically - all start out the same. Even with CAM, there may be hand-retouching that would differ from die to die.
After they are placed in use, markers come from damage to the die that accrues in use.
The markers change over time and that lets you put them in sequence. A die chips, and then the chip grows over time (especially
Cuds). This is called the emission sequence.
Cuds on Coins has some samples as does VAMworld.
Then when dies are used together, this creates a marriage. Obverse Die 1 with Reverse Die B. The Liberty Seated (LSCC) and the Early American Copper (EAC) have done a lot of work in these areas. For a well studied coin, a new marriage is a major event. Reverses (which don't have a date on them) have been used many times over multiple years.
-----Burton
50+ year / Life / Emeritus
ANA member (joined 12/1/1973)
Life member: Numismatics International, CONECA
Member: TNA, FtWCC, NETCC, EveryCountry (online) coin club
Owned by three cats and a wife of 40+ years (joined 1983)
Author: 3rd Edition of the Sample Slabs book,
https://www.sampleslabs.info/