The problem here comes from the absolute positioning that you are using. RadFormDecorator is intended to be used from average users who normally do not do advanced styling using absolute positioning which can be quite tricky in certain scenarios.
And yes, you are right - it is indeed meant to be a black box because of the numerous hacks it uses that target different browsers. For example your screenshots are from IE but if you examine FF or Safari, you will get completely different look. It is not possible to document these hacks as they change over time and they are not meant to be know to average users. You could check this blog post
for example. As you can see we just changed the styling of checkboxes and radio buttons only in Safari / Chrome because we found out that it can be improved due to some supported CSS settings. These are changes that happen quite often and the goal is to keep the control simple to use.
In conclusion, the decorator works fine in "common" scenarios and greatly eases the work of the average developer. In certain, more advanced scenarios however, it might be better to disable the decoration for elements that don't look good (you could use ControlsToSkip for that purpose) or not to use the decorator on such page.
I hope this information helps.
the Telerik team