Why does incompatibility occur when form factor is based on ATX design and Standard ATX design?

ATX (Advanced Technology Extended), is a standard for all personal computer motherboards, computer chassis and PSUs (power supply unit), ensuring a high-degree of compatibility with regards motherboard mounting points, the power supply to the motherboard and motherboard connectivity with peripherals, both internally and externally to the chassis.
Incompatibilities only occur when mixing ATX form factors. For instance, a microATX chassis can accommodate, at most, a 9.6 x 9.6 inch motherboard. A full-size ATX motherboard is 12 x 9.6 inches and therefore requires a full-size ATX chassis which can accommodate several form-factors, including microATX.

Despite the standardisation, incompatibilities can still occur with like-for-like ATX specifications. For instance, a poorly-designed placement of the internal hard-drives in a chassis often interferes with motherboard layouts with regards connections and peripherals. Often the only solution is to replace the motherboard or the chassis, or even both.

Although many such problems are the fault of poor-chassis design, poorly-designed motherboards can also cause problems even in a well-designed chassis. For instance, SATA hard-drive connections are often placed in locations with limited accessibility, such as immediately behind the graphic PCI Express port. When purchasing a top-end graphic card that can easily extend 8 inches across the motherboard, this can severely limit the number of SATA connections that are possible. Many poorly-designed motherboards will only allow top-down SATA connectivity in an array of 2x2, 2x3 or even 2x4 connections, thus making it impossible to use more than 2 elbow-connectors (the only solution to overhead interface). A well-designed motherboard places all SATA connections along an edge of the motherboard, allowing side-entry connectivity rather than top-down entry, thus minimising interference from above and increasing accessibility to those connections.