Most of the time you learn the IPC-A-610 stuff first...then J-standard is an addition.

One thing to remember though is often Mil spec or custom builds actually require better quality than IPC or J-std gives. IPC/J-std are "Minimum acceptability requirements"...meaning "How bad can it be before I am required to fix/scrap the part?" Every time you rework a board you damage it (they are actually being damaged every time they are heated) so you only want to rework if absolutely required.

I can only speak for my personal experience, but we started with the J std but that may be just because the nature of the work was almost exclusively spaceflight.

As far as “minimum requirements” I completely agree. As with all specs, they define the lowest level of acceptable characteristics. Especially if done by contractors this will be the aim since they rarely make additional money going above and beyond minimum standards, but can often lose money doing so