I am glad you are able to learn songs by watching YouTube videos. YouTube did not exists when I started learning to play so I did not have that option. It is an excellent resource for learning to play cover songs on an instrument, but as your questions suggests, it fails to provide a lead sheet, or notation for future use.
I create my own lead sheets for cover songs - even if many versions are available on line. By creating my own I can pick the best chords that seem to work (and that I can actually play), and I can put them on my sheet in a specific place that helps me remember the timing.
The method I use combines technology (word doc on computer, copy and paste, internet search for lyrics - with old fashioned means (pencil and paper). My method does not require any ability to read music notation because the timing is tied to the lyrics - which to me is easier than counting measures and keeping up with the number of beats per measure and half notes and whole notes and quarter rests and half rests etc.
If you want to become a professional musician and play in an orchestra with other professional musicians, you will want to learn to read music notation. If you want to learn to play some of your favorite songs by then end of the week or the end of the day, my method will help you get there without music lessons or a degree in music.
Here is the process I might go through if extracting information from a YouTube video.
First, I Google the lyrics for the song and find them online in a format that I can make use of. Then I copy and paste the lyrics into a word document or open document from the free "Open Office" software. Then I reformat the lyrics to justify everything to the left and add a space between each line (to make room to write chords above the lyrics) and change the font to my liking, and enlarge the size of the text.
Once I have my lyric sheet the way I want it, I go through the YouTube video with a pencil (not an ink pen in case I need to make a change) in hand and write the chord names (C, D, Em, F#dim, etc.) above the lyrics in the exact place the chord change occurs as it relates to the lyrics.
For licks I will skip enough lines in the lyric sheet to past a copy of tablature lines on my lead sheet and use the pencil to make the tab notation. I keep a copy of a blank tab line on my computer and I can use the snipping tool to snip just the amount I need and copy and paste it into my sheet wherever there is a lead break. Then I just write the numbers on the tab lines to indicate which strings and frets to play for the lick.
Once I have all my chords placed where I think they should be, I get my guitar and play along with the video while following my sheet to confirm I have correctly placed all the chords according to where the changes occur. If I discover that I put a chord in the wrong place, I can erase and move it.
When I am confident that my lead sheet is correct according to the way I want to learn and play the song, I will either go back to my word document and type in the chords that I hand wrote with pencil, or I will scan my partially handwritten sheet and save it as a pdf. I also put it in a sheet protector and put a hard copy in a three ring binder.
If the song uses a chord I don't use often enough to have it memorized, or uses a less common voicing of a standard chord, I will make a note of that chord on my sheet (in the bottom margin or sometimes on the back). I often use this format for notating chords on the fly
320003 = an open G major chord
X32010 = an open C major chord
XX0232 = an open D major chord
and so on.
The strings are left to right starting with the Low E string and the numbers indicate which fret. X means mute or don't play that string.
You can also copy and paste blank chord charts into your lead sheet and draw the fretting indicator dots with your pencil to serve as a reference for how to play chords that are non standard or unfamiliar.
Or you could go to a site such as Free Guitar Blank Paper and download sheets such as the one shown below (I took a picture of the pdf and made it small enough to fit below). A sheet such as the one pictured below can be attached as a reference tool to a lead sheet that shows the location of all the chord changes. You could use it to note the licks (lick 1, lick 2) and any chords that are less familiar.
I realize this is not the high tech software based solution you asked for, and you can certainly use those as well. But this method works best for me when sitting in front of a YouTube video and trying to place the chords in just the right place. I only have one computer and if I am playing a YouTube video, it's easier for me to have a sheet of paper and pencil on the desk so I can make my notations as I watch in real time instead of toggling back and forth between a software program and the video. Old folks like me who have a similar question may find this solution to be helpful with less of a learning curve than an all software based system of notation.
I hope you have tons of fun learning more and more new songs and expanding your repertoire on guitar!