No, there would only be a problem painting areas of your house different colours and then going over them with a solid stain (or another paint) if you used an INTERIOR oil based paint on wood outdoors. All three conditions would have to be present to have a problem: the paint you use would have to be an interior oil based paint, and it would have to be applied to wood outdoors.
If you used an exterior oil based paint, or any kind of latex paint (interior or exterior), or painted over any other substrate (metal, concrete or plastic), then you shouldn't have a problem.
Here's why:
The primary difference between interior and exterior OIL BASED paints is that exterior oil based paints will crosslink less densely to form a softer, more elastic film than interior oil based paints. This is necessary because wood outdoors will swell and shrink with changes in it's moisture content caused by seasonal changes in temperature and humidity. So, a paint that is too hard and strong won't be able to stretch and shrink with the wood and the result will be that the paint will soon crack and peel. Temperature and humidities indoors are much more constant and so you don't have the swelling and shrinking of wood like you do outdoors, and so oil based paints meant for indoor use will dry to a much harder and more rigid film which provides better protection and stands up better on working surfaces such as shelves and even floors.
Both interior and exterior latex paints are far softer and more elastic than you need to stretch and shrink with wood expansion and contraction, so the primary difference between interior and exterior LATEX paints is the addition of UV blockers and mildewcides to exterior latex paints. Also, because inexpensive latex paints and general purpose primers will typically be made of the same plastic as white wood glue, which soften up and loses it's adhesion under wet conditions, exterior latex paints will always be made from the same plastic as Plexiglas, which is highly moisture resistant.
So, if you were painting over metal or concrete, any paint could simply be painted over because there won't be the dimensional changes you find in wood outdoors. Thermal expansion of metal and concrete (and even plastics like PVC) are very small compared to the expansion of wood with seasonal changes in it's moisture content. But, if you're painting over wood outdoors, then you have to use a paint that will stretch as the wood swells and shrink as the wood dries, and if whatever paint you use is too hard to stretch and shrink, it'll crack and peel.
BOTH exterior latex and oil based paints will have UV blockers and mildewcides added to them. The UV blockers are normally iron oxide extender pigments that are transparent to visible light but opaque to UV light. It's the opacity to UV light that protects the paint film from damage from UV light. Mildewcides work by having a high affinity for water such that the powdered mildewcide added to the paint actually migrates towards the wet surface of the dried paint film and kills any mildew spores that land on that surface before they have a chance to grow. The RATE at which the mildewcide migrates through the paint film is called it's "leaching" rate, and lower gloss paints, being rougher, have a larger surface area and hence a higher leaching rate. It's critical to match the mildewcide with the binder used in the paint to obtain the minimum leaching rate that is still effective at keeping the paint mildew free, so this business of buying a bag of M-10 mildewcide at a Sherwin Williams Store and just having it shaken up with whatever paint you buy is stupid. It takes a lot of testing to match the right mildewcide with the right binder to get the optimal leaching rate for the best paint performance. People that simply add a bag of mildewcide to any paint are only interested in it lasting until their 1 year warranty expires.
I don't know anything about exterior house stains.
Keep in mind that if you were to paint patches of your house with an oil based paint, you'll need to paint over those patches with an oil based primer or sand the paint down before painting over those patches with a latex paint for proper adhesion.