Holes in the floor will lower the waterline somewhat. The amount will depend on a few factors, such as packraft model/size, paddler weight, and weight of gear carried. The best way to find out is to make a small hole in the packraft’s floor (where you plan to place one of the drain holes), load up the packraft with your typical gear, and then sit in the packraft until the water level inside the cockpit equilibrates with the water outside. That will be the maximum water level you can expect in flat water. (If you’re not ready to commit to making holes in the floor you can use a hose to siphon water into the cockpit from outside.)
Depending on how well your self-bailing floor displaces water, it might add some additional flotation after it’s installed, so the relative water level in the cockpit might drop a bit.
In my opinion, self-bailing packrafts are best suited to whitewater paddling in warm climates. The main advantage of a self-bailing cockpit is that water drains out naturally when waves crash over the tubes and fill it with water… it’s not really meant to keep the paddler dry. As you paddle through waves, water can slosh around in the cockpit and even surge up through the holes in the floor, above the flat water static equilibrium level, leaving you with a wet butt even if no water splashes in over the tubes. For this reason, if staying dry is one of your goals, I wouldn’t recommend a self-bailer. If you just want to add ballast to change the handling characteristics, water-filled drybags might be a better option (or use the old solo canoe paddling trick of placing some rocks on the floor near the bow).