Time machine space questions, not the same as Activity Monitor

Hello
I am new here and kindly ask your thoughts on what I am seeing.
I have a 13" MacBook Pro early 2011 with OS 10.7.5
Earlier this year I tried an upgrade to a new OS and experienced a failure that required me to make a visit to the Apple store.
I believe they reinstalled the OS and if I remember correctly I just did a recovery with the Time Machine backup I had.
While that backup was not very recent, yea OK I get that was stupid, what was odd was that not all my files were backed up.
I lost a significant number of files from April 2013 until the time of the failure in 2014, for reasons I have no clue as to why.
My Time Machine does not have any excluded files as far as I can tell.
So my first question is:  Can anyone help me understand what may have happened and how to counter that?
Then yesterday I decided to invest in a new backup external drive.
During the process of setting it up and doing the 1st Time Machine backup on that, I noticed the following:
In Activity Monitor under the "Disk Usage" tab shows the Macintosh HD as using 258 of 319 GB, and then selecting my user name it shows using 578 of 639 GB.
When I did the backup with Time Machine it backed up approximately 250GB.
I thought Time Machine backed up the entire HD.
What is the difference between the Macintosh HD space and the user space in terms of usage and total?
Should I be worried or visiting the Apple store again?

OK, done.
I created a text.txt document containing the words "Version 0". I saved it to the Desktop, closed it and selected "Back Up Now" from the Finder.
Waited for that to complete, opened the test.txt document again, modified it by adding the words "Version 1", saved it, closed it and selected "Back Up Now" again.
Repeated that twice more, so the end result was a Text.txt containing the words "Version 0", "Version 1", "Version 2", and "Version 3".
I expect that I should now have three versions from which to choose to restore, all from different times, plus the latest one still on the Desktop.
Creation and backups now complete, so the next step was restoration:
From the Finder, I used "Enter Time Machine" and verified that I had four different recent times from which to choose. I chose the original text.txt document and elected to "keep both files". It restored the original, which I opened and verified it contained nothing but the text "Version 0".
I repeated this for the subsequent version. I opened that one and confirmed it contained the words "Version 1".
I repeated this for the subsequent version. Now I have three restored text.txt documents, plus the one on the Desktop.
I opened all four text.txt documents and stacked them as shown in the following screenshot:
Conclusion, no surprises that I can determine.
Is this what you had in mind, or was there something I did that was different from what you need?

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