I presume by factories you mean large chain type kitchen companies? I work for a small kitchen company that manufactures everything and I know we use different construction methods and materials to that of larger companies. For instance, we use solid backings rather than the Masonite backings. We construct the carcasses differently - mass produced may be cheaper but the quality & effort put in to the craftmenship is not there. We will also make units to custom sizes that suit your space rather than only having a set range to chose from - large factories will have mass production lines and will not custom size anything. You'll have options of 150mm, 300mm, 400mm, 450mm etc which is not always ideal.

Custom cabinets can be made for any space (width,etc). The factory cabinets are all standard and are finished (stain/paint) at the factory.

Standard cabinetry ( factory in your words) are basic sizes. For example; Base cabinets will have a standard height and depth and the widths are standard; 18", 24" 30", 36" and so on.
The "box" is somewhat standard and the doors are what really "make" the cabinet and affects the price.
The quality of the "box" will change with certain manufacturers.

Many kitchen layouts can accommodate standard cabinets but sometimes, you need a custom cabinet. I use a cabinet line called Custom Wood Products which is a semi-custom cabinet product. So, they take the basic cabinet and will modify it to your design and specifications.

Customs cabinets are available via carpentry shops and have a reputation for being very good quality. These are comparable with the Custom Wood Products line in price.

I've attached 2 files for a Kitchen that I designed. The BEFORE is standard cabinets and the AFTER is a combination of standard and custom.

I hope I've helped you answer the question.
Eileen

Whatever you choose, make sure you request lots of drawers.

All the different “levels” of cabinets can be so confusing! Here is a great article comparing the 3 modes: http://bit.ly/1rWygrs

anyone know what kind of doors those are (in above pic - McCandish). I am debating about Shaker vs. raised panel, and I've been seeing a lot of these (the second pic - cream cabinets) and would like to know what they are called. They are a little dressier than Shaker, and yet, still a nice clean line.

they are called Raised Panel. Good luck!