Continuing on Interior Woodwork

I posted this on the Cruiser's Forum to get some answers. I figure I'd post it here to see if any readers can offer an opinion: In the process of restoring Windsong I have been taking home pieces of interior wood and trim to work on when I have time. All of the interior woodwork was stained with a dark reddish hue and didn't appear to have much of a finish coat of varnish or anything. The woodwork is mostly teak with a few mahogany pieces.

For an example, here is a teak cabinet door and its trim taken from the v-berth. The lighting doesn't show how dark and ugly the stain is, but you get the idea.

For each piece I clean the wood off then strip the old finish and stain with a chemical stripper. After stripping I sand the piece down to 220 grit all over and end up with some nice looking wood:

with a bigger cabinet door & trim:

My question now is what do I do next?

My current plan is to use Minwax Helmsman to finish, but am unsure about how to start. They recommend using the Minwax stains for a first coat and if I want to keep the color of the teak I assume use the "natural" stain. But there are a few areas where there are nicks and dings which will need to have wood filler applied before finishing. Will a stain be necessary for these patched ares to not stand out? Will this require me to stain all of the wood a darker color for uniformity?

Would a few thinned layers of the varnish do the same thing to seal and provide a base layer? Or would their brand of stain work best as a base coat?

My other concern is the trim. As you can see in the photos, the trim has large holes for the screws which were bunged when attached to the boat. I am nervous about applying finishing to the trim when I will need to affix bungs later on. I figure putting the bungs in and sanding them down flush would ruin whatever finish I put on the trim. So would it be a good idea to install the trim raw, bung, then finish; or finish the trim, bung, then patch whatever areas were sanded down? My concern is the finish around the bungs would look different to the surrounding areas that didn't get the sanding/refinishing.