Perhaps you need a stipple brush. These are most often used for stenciling, but are also used for other paint techniques. A stipple brush applies paint in an up and down motion which might be better at getting paint into the holes. Here is a picture of two types. The one on the right is typical of stencil brushes while the one on the left is most often used on walls. I do not know that this will fix your problem, but it's the first thing that came to mind.You might be able to thin the kilz with water. Thinner paint is more likely to flow into the tiny holes. Also try using a sponge to apply the thinned paint.

Do you have plans for the niches next to the fireplace? Maybe builtin storage cabinets and TV on a pull-out swivel on the right. The L side you could leave blank or have shelves above the lower cabinet. It will add some architectural interest and allow for storage. Then a seating area in front of fireplace - sofa and 1-2 chairs. A small desk area in the space between sofa area and dining. Though I’d probably have a computer station that closes off (do you need for desk top or just lap tops?)

Really nice house. You could remove (but not discard) the existing mantel and live a while without, taking the time to consider all your fireplace options, including a more bulky but less wide mantel that is a part of a fireplace surround. (The current mantel could be reused as support for shelving or a new mantel.) Would not paint or widen the existing built ins Would not paint the wood around the cased door opening to the entry unless you do decide to put white (or wall colored) built ins on that wall incorporating the tv behind where the floor lamp now stands (third pic). If you do keep the built ins beside the fireplace their current wood look, then definitely leave the baseboard the treated wood to match the built ins. If you paint the current built ins white, then paint the window trim white, too; however, otherwise, if the current built ins are going to stay wood as is, you could decide to paint the window trim white only if you're not going to add drapes that would cover most of the window frame anyway. Would definitely paint the trim at the top of the wall the wall color since ceiling white could visually shrink the height of the room. As you consider wall colors, in addition to considering blue or gray, you might consider a wall color that is a tan (but without pink or yellow hue) such as the lightest color in the stone in the fireplace -- and keep the ceiling white. If you paint the new built-ins surrounding the tv either white or a light wall color, you should seriously consider updating the ceiling fan with one that is silver metal and tinted semi-clear plastic/vinyl blades. As to the front porch, does any part of the floor of the existing stoop extend beyond the front wall of the house or do the steps start as you walk out the door (as the sloped rails suggest)? Something you might consider is building a treated lumber deck over the steps from the front wall of the house to the sidewalk from a point midway between the door to the right front corner of the house, with wooden steps leading from the side of that deck to the sidewalk and having it built with posts extending above the deck for the railing and to build to in order to add a porch roof later.

We’ve been moving the past few days so they can start demo tomorrow :) I’ll try to get a drawing and inspo pic loaded once we have our internet up and running at our temp location.