The Ins and Outs of Caulking states that compatibility between substrates and sealants involves two issues. The first is sealant adhesion to substrates (which may be dissimilar); the second is the potential for uncured sealant to damage the substrates (by chemical action of a component in the uncured sealant).
Silicone sealants are recognized as adhering well to most non-porous substrates. Their effective adhesion to porous substrates like wood or masonry may, however, require the use of primers. Polyurethane and latex acrylic sealants are generally recognized as adhering relatively well to porous substrates like wood and wood-based products without the use of primers. Sealant primers are rarely if ever available at hardware stores and home centers. A quality primer paint, suitable for the (porous) substrate, usually improves sealant adhesion. If end and edge cuts on siding or trim surfaces are primed before the siding or trim is installed, the priming is significantly more effective.
The chemical components of sealants with the potential to damage substrates are most commonly either organic solvents or acidic constituents. The organic solvents used in most sealants are not sufficiently aggressive to harm most substrates. The smell of vinegar in uncured silicone sealant indicates the presence of an acidic constituent. Most substrates are unaffected by such acidic-cure silicone sealants, but a few are. Installation instructions for components such as fenestration units may indicate if sealant use is recommended, and if so, what type of sealant to use. Use of a different type of sealant than recommended by the manufacturer may result in chemically induced damage to the component. Some silicone sealants are unsuitable for certain porous substrates because they can leach oily materials, resulting in staining.