Start by taping the hole IN the mast step tube, then flip the hull and repair that hole on the exterior... fair out an oval around the hole, pre-cut some appropriate-sized patches from matt or cloth, get your resin & catalyst ready, and handle your business. If that hole in the step goes clear through to the outside of the hull, with no leakage into the hull void itself, you may be able to fill the hole, using chopped-up glass and catalyzed resin... just wet or fill the hole first, then gently stuff as much chopped-up glass as you can into the hole before placing your patches on the hull exterior. You will have to make sure that this is feasible first by performing a simple leak test, as you do NOT want to simply pour expensive catalyzed resin into the hull void without solving the problem. However, the possibility does exist, and it will make your job that much easier.
If there IS leakage into the hull void, then maybe you're better off using a thick filler for the hole itself, something compatible with glass layers on top. Others will probably chime in here, but if that "thru hole" is limited to the step tube and hull exterior, with NO leakage into the hull void, then go with my first suggestion. Once you're done with the outer patch, flip the boat again, level her out, remove the tape, and pour some catalyzed resin into the mast step tube... try NOT to get any resin on the wall of the tube itself, carefully pour right down the center so you add some protection to that worn mast step base or foot. Afterward, go with Lali's suggestion to add a disc for extra protection. Some outfits make these discs, I just used a large reinforced rubber washer I found in my tool cabinet back in Coronado. You can find those reinforced rubber washers at any industrial warehouse, and probably at stores like the Depot as well.
This is a fairly simple, straightforward repair job, you should have no problem knocking it out. If you've never done any glasswork before, just read up on it on the web or here at this site, and pick a good day for it... sunny and 70 degrees would be good, and no wind if possible, keeps the bugs & dust down. Have all your materials at hand: resin, catalyst, glass matt or cloth (or both), disposable latex gloves, disposable resin pot (yogurt container or something similar), rags, acetone, etc. I always placed a broad low cardboard box nearby so I could toss stuff into it as I went along... just my own way of doing things. You may have to swap out gloves as you do this job, should yours get too gunked up... with care, that shouldn't happen, since this job is not that difficult. You're not working blindly on any section, though you DO have to figure out whether you can fill that hole as I suggested. You'll figure it out, I have faith in ya... LOL.
BTW, if you live near a surf shop, they can probably tackle this sort of repair too... my friends ran a shop in Coronado for three decades & more, and boats were commonly seen in the yard out back, all in various stages of repair. I even dragged my boat up there now and then to work on her, but I did all that work myself, my friend just turned me on to the resin, catalyst, glass cloth, etc. WTF, he used to buy 55-gallon drums of polyester resin, that's how fast he went through the stuff with constant board & boat repairs being made, LOL... so he never missed the small amounts that I used, and I usually found enough glass cloth in the scrap box, so I didn't have to cut any off the rolls. Having said all this, you should NOT be intimidated by this simple repair, it is NOT rocket science and it isn't even that difficult, compared to some more complicated repair jobs one can do with a Laser. Do it yourself, you can easily handle it... CHEERS!!!
P.S. You'll need a "stir stick" for your resin & catalyst, a clean wooden popsicle stick is perfect for the task, as it can also be used to apply small amounts of catalyzed resin where ya need it. It also serves to smoothen out wrinkles and whatnot... remember, NO AIR BUBBLES in your work, they are VERBOTEN! By wetting up all surfaces thoroughly, wetting up each additional layer, and smoothing out wrinkles with stick or gloved finger, you can avoid air bubbles and their associated weakness. Learn to mix only as much resin & catalyst as you need, so you're not left with excess unused resin... it all costs money, LOL. Post some pics as ya go, not during the actual task but afterward, as the resin is curing... or simply show us your results once the job is done. Moi, I'd probably use a small amount of paint atop the repair, just for added protection... mask off a small area that covers the ugliness. A diamond with rounded corners, perhaps... or go the bourgeois route & leave it, nobody will ever see it unless you capsize, LOL.
Yes, of course you need to patch it, a quick fix from the outside should be easy. In the long run, though, you want to restore the inside of the mast step to the original level, and protect it with an anti-abrasion disc. Does the step leak water into the inside of the hull?