Why are there different Ethernet PHY magnetic configurations?
Schematic 1 offers direct connection to the center tap of the exterior
port windings, and is suitable for PoE connection (which may either
draw power, or supply power, over twisted pair).   Schematics 2 and 4
do not have low-resistance connection suitable for PoE.   Schematic #3
does technically have the ability to connect to PoE, but only
through an inductor (which may saturate).

Modern designs would usually allow bidirectional use of
the four lanes, and #2 does not.   It is not surprising that it may
become obsolete, in favor of #4.