Yes , This would be possible now (July 2018) .
First you should create 3 Buckets on S3 , 1 for input , 1 for output and 1 for the thumbnails , Next you should create a pipeline to link your input bucket to your output bucket , Next you should create a Job on the pipeline using AWS elastic trans-coder,
When creating a job make sure you specify multiple inputs (with matching file types) If you want to use different file types it is also possible but it will take more time , Pipelines can hold multiple Jobs , so you should first create a job that trans-codes all videos in Bucket A (input bucket ) to the same file format in Bucket B (output bucket ) , to continue with concatenation you specify 2 inputs foo.mp4 and bar.mp4 and make sure you only specify ONE output , after you create your job check your output bucket and you should see your video.
NOTE: when choosing the output preset make sure it matches both your inputs and outputs