Q.My indoor Madagascar palm continues to branch at the top despite pruning them. Should I continue to prune?
It also loses its leaves in the winter and regrows them in the Spring. The two branches are the only places new leaves grow back. I’m now hesitant to prune the branches. However, it’s about 30 inches high now, but only grows about 3 inches per year. I want it to grow taller and am not excited about keeping the branches, but don’t want to harm the plant either.

You may be able to induce branching in a Madagascar palm tree by cutting the top of the plant. This process requires injuring the center of the spiral from which the leaves normally grow, so that the plant produces two new stems. Cut the plant with a clean, sterile knife or shears to reduce the risk of infection. While most Madagascar palms recover, there is always a possibility that your specimen will not regrow after cutting.
You can increase the chance that your Madagascar palm will branch by providing it with ideal conditions. Planting in full sun, providing temperatures above 60 degrees Fahrenheit year-round and using an extremely well-drained growing medium encourages outdoor plants to develop the extensive root system needed for branching. Ideally, these plants should receive regular watering during the summer and remain relatively dry during the cool season to discourage frost damage and produce an extremely healthy specimen.
https://www.gardeningknowhow.com/houseplants/madagascar-palm/madagascar-palm-care.htm