For the check-box disabled issue, can you try relaunching the utility again? Once run, select the global Upgrade Layouts, Deprecated Control upgrade and Remove in-line style checkboxes. These checkboxes might be disabled for some rules, that happens when the rule is not having that specific component to upgrade.
Then select the global select all for performing the upgrade and then click on the upgrade button.
1. You will find a checkbox as Current RuleSet version (Current RSV) that makes the utility do the upgrade in the same version rather than saving it to a higher version. As mentioned in the call all the layouts are not supported for upgrading to dynamic layouts. Please read through the guide/help bundled with the utility to make sure the pre-requisites are met and the upgrade is being performed only for those supported layouts.
2. The utility generally shows the rules based on the user profile. If the user profile is having multiple versions mapped for the same ruleset then it might cause this issue. Also, check if the applies-to class of these rules is different or same. If all of these are not issues in your application, but still experiencing this behavior then it might be an utility issue which we can take a look and try to resolve in the next release. We might want to have a quick call to understand this issue better.
3. The checkboxes are enabled only when the section rule has deprecated layout, control or inline style. We might have to see why the rule is listed in the first place when none of these checkboxes are enabled. Can you give us the screenshot of one such rule form along with what kind of warning messages it has, so that we can debug why it is getting listed.