You are wise to doubt your builder. I do this work for a living and I can tell you that some of my prettiest floors have been those with lots of character. And, yes, there are fill materials which will not pop out. Timbermate is just one and...yes...some of us use epoxy and some home brews. 3M is just one manufacturer of clear epoxy and West Systems is another. And, I have heard that someone is now making a colored epoxy as wood fill that I have not yet seen or used.

So, the short answer is who cares about the "market"...get the floors YOU want.

Find a floor finisher who will do the work you want done the way you want them done.

West Systems is easily tinted when needed.

Depending on how large the fill area is, making them larger and disguised as a knot often looks good.

Trying to make them 'match' is almost always a failure.

'Graining' is not a talent that is available very much.

Thanks for the replies! I suspected there was an alternative. It just didn't make sense otherwise.

brickeyee, what is graining? I googled, but just got info about faux finishing other surfaces to look like wood.

if you read comments on this forum its often recommended to find products with character as it tends to hide the inevitable ding or dent. People are often more upset with the clear grained products as they tend to show everything.

I agree with boxers re: clear grained products. If it looks like a furniture top, you can be sure that it is going to show every ding, dent and minor scratch. Most of the exotics (rainforest wood) show wear and tear from day one. I won't sell and install floors from rainforest sources for my customers for lots of reasons, and I wouldn't install it in my own home for the likelihood that it will show wear and tear sooner than other choices.

"what is graining? I googled, but just got info about faux finishing other surfaces to look like wood."

That is the overall definition, but it also refers to making a repair match the grain of the wood around the repair.

It is done on furniture repairs to help conceal the repair.
Japan colors, permanent markers, even tinted shellac all can be used to make an otherwise uniform color repair blend into the surrounding wood grain.

A really well done repair takes very careful examination, sometimes with magnification to detect.

For floors disguising the repair as a knot works very well, since the view is from standing height.

If there are a lot of knots a well done repair will blend right in.
Just be careful not to make the 'knot' perfectly round or far off in color from the real knots.
Using a color that matches the real knots (possibly with a little speckling thrown in if the real ones have any) and folks will be hard pressed to spot the fake without crawling on the floor.