Questions Ab Initio

You can use components that does not require any sorted data (explicit or in memory sort) to get pipeline parallelism. Like Reformat,FBE, Redefine components. And Components that needed sorted data like join, roll-up, merge, sort, partition by key and sort breaks the pipeline parallelism.  

Use Sort within Groups only if records within a group are processed before being sorted on a minor key. i.e. if processing "A" needs records to be sorted on field {"1"} and later in the flow processing "B" needs records to be sorted on field {"1", "2"}. In this case before processing "2" and after processing "1" use sort within groups with major-key as {"1"} and minor key as {"2"}. If records are not grouped to start with, use Sort with a multi-part key. There is no benefit to using Sort within Groups directly after using a Sort component.

In output index of reformat use logic if next in sequence % 3 == 0 then output add trailer from in1.    you can use normalize generate length as 2 when next in sequence %3 ==0. 

Kill is for unix process and m_kill for ab initio graph. kill needs process id, and m_kill needs rec file name which is easy to find out, and may be it would be doing something more in backend, like waiting for AB_TIMEOUT

Which ever path is provided in layout option, will be used to crate intermediate files.