The final grade is the only thing that makes the transcript and is usually what programs focus on. For example, Mayo has developed a fairly complex grading system but the 3rd year clinical grades are weighted more heavily than many other parameters (points given in descending order for honors, high-pass, etc...).
For those programs that are less "scientific" about it then not having "Honors" can be more problematic but remember it is usually not just one variable that is scrutinized - it's the whole package. If you have a low USLME step 1 score and no clinical honors in your 3rd yearc that can be a very difficult hole from which to escape - if on the other hand, you have a high step 1 and no clinical honors you can still be in the running depending on the rest of your application (undergrad school and performance, med school and performance, orthopaedic research, presentations, publications, etc...).
So in the end, the step 1 will get you past the initial screens of many programs but it's the whole package thereafter that will push you into the "interview" vs "no thank you" group.

Good luck and hope this answers your question - -

wnl