When on a run and finding any work bench or cooking station, if I store all junk there, will be available in the Sanctuary work bench? Or is each work bench inventory specific to that area?
Crafting stations do not inherently link to the one back in Sanctuary. However, some have the option available, through supply lines.
If the crafting station is in a settlement you own, the crafting stations will be linked with any other settlement linked via a supply line. For more information on setting up supply lines, look to this question here.
Without a supply line, especially in regards to crafting stations at locations you do not own, items are only shared between the local crafting stations. In other words, the armor workbench will share with the weapon workbench in that area, but not with Sanctuary or any other location.