Thank you gentlemen for all the input and comments. I'm seeing my posts could be more concise so after confirming my data, it's probably best if I summarize what I'm seeing and post the spreadsheet based on the download & install runs I put together. Not sure if any of this is on purpose or if some of what I'm seeing are tool errors, just passing along observations by comparing what the tool downloads and installs.
1. NET 3.5.1 updates between 2015-05 & 2017-04 not installing
2. When downloading (selecting security only downloads), 303 updates up to and including 2020-01 are being downloaded. Only 159 of those are installing.
3. When downloading (security only downloads selected), all Security only Quality Updates are downloaded. However during the install run, 4 are not installed (kb3212642, kb4056897, kb4074587, kb4088878). These 4 do not show as superseded per update catalog and are not installed in further runs either.
4. The 2020-01 IE Cumulative Security Update does not download
5. The 2015-01 Security Update kb3021674 (Vulnerability in User Profile Svc.) does not download. It is replaced by the 2020-02 Security only Rollup that does not apply to systems unless the an ESU license is active.
6. There are a total of 13 .NET Security Quality Rollups & Security Only Updates dated between 2015-01 to 2020-01 that do not download. Of those, these 10 are not superseded (kb4014985, kb4019108, kb4041090, kb4099637, kb4340004, kb4345679, kb4471981, kb4487121, kb4498961, & kb4507411. Originally I thought these would be addressed by the 2020-01 .NET Rollup, but kb4534976, kb4535102 were not found either. In addition, .NET update kb4041083 that was not found. it is replaced by an update (kb4055432) but that one was not part of the download so not installed either.
7. The 2020-02 SSU installs 2x (once on install run 5, then again on install run 8)
8. When downloading (security only downloads selected), included are Security Quality Monthly Rollups. Other than adding about 2gb to the instance, I'm not sure if this is causing further install issues.
9. When downloading (security only downloads selected), kb3191566 is not downloaded so doesn't install.
It might help to have a visual reference so my comments are clearer. Ive uploaded a .xls spreadsheet showing the history here and the logs are shown on earlier posts.
https://www.dropbox.com/sh/1z94toy0g00huan/AAB-k2sv8Mn6RaegCGnfuRO1a?dl=0