I'm not sure how the alignment issue arose. It may have come about during the time when "AF" format drives were introduced for HDDs. I really can't say.
But I still use an Acronis Disk Director 11 Update#2 released around 2011 (before the Update) to prepare an SSD for use or more specifically for cloning, and it assures proper alignment.
But here's my advice about cloning one OS boot-system disk to a fresh SSD.
Run a thorough CHKDSK with repair options on the old SSD (or HDD). Use SFC /SCANNOW to determine if there are any files on the disk that are corrupt or need repair -- and hope that SFC does the repair.
Then, one by one, fix all the red-bang error events in your Windows System event-log, except for any you might determine are benign. And perhaps you might check the Windows "Application log" for similar problems to see if they persistently re-occur. If they seem to derive from some software installation, uninstall the software or update to newer versions.
Once your event logs are properly "in the blue" with some routine yellow "warnings" or "benign red-bangs," clone the drive. If you're cloning an HDD to the new SSD, defragment it before making the clone.