"Can GL-5 gear oil be used in an application where manual transmission fluid is recommended?"
The American Petroleum Institute (API) GL rating system is intended for gear oil specifications. While a manual transmission does in fact have gears, it may also contain other components such as synchronizers. The gears and synchronizers have seemingly conflicting requirements. In general, the higher the GL rating, the higher the extreme pressure (EP) protection provided. This is great for reliability and wear reduction in hardened gear sets, but it can spell disaster for synchronizers.
EP additives are often made of a sulfur/phosphorus compound that will adhere to metal surfaces through polar attraction. Once they have coated a metal surface, these additives need only to be introduced to heat and/or pressure (from a collapsing lubricant film) to spring into action and start doing their job. In a hardened gear set, this adds a great deal of wear protection as well as life and reliability to the component.
However, because of the mechanism in which these EP additives work, when they are introduced to softer yellow metals, the results can be disastrous. They attach in the same manner (metal-wetting polar attraction), and when heat and/or pressure is introduced, the additives will chemically attack the softer yellow metals. This aggressive attack can prematurely wear out synchronizers.
GL-4 products typically use about half the sulfur/phosphorus additives of their GL-5 counterparts. This means they provide less protection for the gear set but do not damage synchronizers quite as severely. When a GL-5 gear oil is used in a manual transmission that contains synchronizers, you can expect to find two to four times as much copper in the used oil analysis report in comparison to a GL-4 oil. Eventually, the synchronizers will wear to the point that they no longer make contact with the other half of the cone, bottoming out before stopping the opposing gear.
So while an API GL-5 gear oil can be utilized in an application where manual transmission fluid is recommended, there will be a tradeoff. You can anticipate excellent protection for the gears but also a reduction in synchronizer life if these components are made of softer material.
Generally, you should heed the recommendations made by the manufacturer. Issues such as those outlined above are considered during the components’ design phase. Manufacturers usually have all the information required to make educated decisions, which are then incorporated into their recommendations.