I'll reply to each objection, if I may.
- Even after troweling a filler, the equipment will ultimately knock most of it out duing the screening steps of finishing or further sanding.
Not true. If fillers did not stay in the holes, people would stop buying them. You need to use the right ones.
- Sinking any nails may damage (split) the already once/twice sanded 3/4" boards. (Remember though that most are already sunk!)
It's possible to split some wood when setting nail heads but it depends on the size of the nail head (large or finish?) and it would mostly happen on the end butts or next to the edge of the board. It could happen.
- If using a trowelable filler, it may also fill the grain in areas, which would look bad when finished.
Simple answer. Don't use a trowelable filler. Spot fill only. Use a 3" putty knike and just fills holes and areas that need it. I do this ALL THE TIME. Typically, I'll fill the holes before edging and final finishing. I don't leave filler behind in the grain.
Originally, 100 years ago, the nail holes were not filled. "It was important then to show off the hard work of all the individual nails".
I've worked on top nailed, 5/16" floors that were over 100 yrs old and their nails holes were filled. I can't say about your area of the country.
We are not staining so he thinks that any filler will not really match and "you will see them anyway".
If use use a filler color matched to your wood, it should match pretty good. Yes, close scrutiny will tell it's got filled holes but I assure you, it looks better than dark, unfilled holes.
I would appreciate any thoughts. Were the floors really not filled 100 years ago when new? If that were true, preserving historial accuracy may be important.
It depends on the area and the wood. In New England, many old pine floors were face nailed and those holes were not filled. But those floors were the subfloors and finished floors which the wealthier covered with rugs. If the floor was meant to be a utilitarian type floor, then using filler may not be historically accurate. I would suggest more research on this aspect if it is important to you.