I don't know if this is true for all Pine lumber, but Southern Yellow Pine (and all woods with a notable yellow or reddish colour like cedar, redwood, red oak yellow pine, etc.) are that way because they have a lot of "tannin" in them.
Tannin is brown in colour and is soluble in water. As a result, people who use a latex primer and/or latex paint over such woods will often find a brownish stain on the primer or piant. This is because the tannin in the wood will dissolve in the latex primer or piant and diffuse through the wet film thickness before the primer or paint dries.
In painting situations, the usual fix is to use an oil based primer to prime such woods first. Since tannin doesn't dissolve in mineral spirits, tannin won't discolour an oil based primer. However, I'm not sure how you would overcome this problem using a water based product, but I expect the are water based products or alcohol based clear coats that dry very rapidly that will allow you to establish a seal between the wood and any water based clear coat you apply.
Water based coatings like the Diamond Finish that was mentioned don't yellow with age the way oil based coatings do. People often avoid using oil based coatings for that reason alone, but it's not always justified.
That's cuz yellowing of oil based coatings is generally misunderstood by most people. Yellowing only occurs where there is little to no direct or indirect sunlight present. Where you have direct or indirect sunlight, such as on a window sill, there will be no yellowing of oil based coatings because the sunlight will bleach the yellow out of the coating faster than it forms. Also, the yellowing of oil based coatings is completely reversible. Museums routinely expose old oil based paintings in their collection to indirect sunlight to bleach the yellowing out which occurs in storage. They do this before putting the paintings on display so that they painting will look the same as it was painted; without a yellowish tint to it. So, if you paint a chair with an oil based paint, and it yellows with age, you merely have to move the chair to a room with more natural sunlight, and in a few weeks the yellow discolouration will have vanished, and the chair will be the same colour it was when it was first painted.