Long story short: A guy from a roofing company who came out to troubleshoot and give an estimate put a tarp on my roof and secured it with nails. He said that the nail holes can simply be caulked when we're done using the tap. Is this accurate? Is caulk a permanent fix for the holes?

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Long story long: I've had a leaky roof off and on for over two years (I've owned the house for 3). The previous owners disclosed that they had water infiltration in the same area of the house, and they used small roofing company A to replace gutters and that supposedly solved the problem. So, whenever I've had the leak, I've called company A and the owner has come out and repeatedly unsuccessful repaired the leak. This time, I finally decided to get other opinions.

A guy from company B came out to troubleshoot and give an estimate for repairing the issue. We seemed very thorough - found several shingles curled (not really curled yet, just loose) that he sealed down, and one cracked shingle four tabs in that we suspect is the culprit of the leak. The roof is possibly soft/mushy under it. He went in the attic to check what damage was up there (which company A refused to do). I asked if he could temporarily tarp the area with the cracked shingle. I was concerned that other people wouldn't be able to inspect under it and the nail holes could cause more problems in the future. He said that the other people I had scheduled would just be able to take out the nails and put them back in the same place, then nail holes could be caulked when the tarp is taken off when the shingle replacement was made, and would be fine. So, I had him tarp it, but that night it rained again and the leak was worse than ever! I suspect it was because he stepped on the cracked shingle, making it worse. In the morning I called him to let him know and he said he could come at the end of the day. (Estimate is ~$380 + $20 for each additional tab)

I had already scheduled company C to come out that next day. A guy came, said that the guy B didn't tarp properly - he left the top edge open, when he should have put it underneath a row of shingles. So, the tarp was useless. He refused to inspect under the tarp. Said he would just write up an estimate for replacing a 10-foot wide swath from the ridge of the roof all the way down. He also tried to upsell more, saying I needed my chimney flashing replaced. (Estimate is ~$1900(!) for including the chimney flashing)

Guy B came back, I explained what guy C said about the tarp. He apologized for not doing the tarping correctly, and said he would correct it. In conversation, I said that guy C didn't want to take up the tarp to inspect the roof; that he would just replace the shingles all the way to the ridge. Guy B misinterpreted what I meant, and TARPED all the way to the ridge! So now I have more nail holes that necessary.

Lastly, I had a third company come out for an estimate, company D. He doesn't think caulking the nail holes is appropriate, and would just replace all the shingles under the tarp. (Estimate ~$700 with a one year (?) money back guarantee).

First, let me say that companies B and D get fantastic reviews. Company C gets okay reviews, but my friend used them and liked them. But, my experience with the guy from B makes me doubt their competence --- unless it's true that caulking is a perfectly fine solution. WWYD?