If you want to run Ellié Computing Merge and systematically get a textual result for your merge, even if there are conflicts, you need to use the inclusive merge option of Ellié Computing Merge.
Inclusive merge is an option which let Ellié Computing Merge save merges with conflicts by interleaving the 2 or 3 sides where there is a conflict, with an output similar to this:
<<<<<<<<<<<<<<
left side text
<<<<<<<<<<<<<<
ancestor text [if this is a 3-way merge]
>>>>>>>>>>>>>>
right side text
>>>>>>>>>>>>>>
You will run a command similar to this:
merge --mode=merge3 ancestor left right --to=output_place --yes=inclusive-merge
NB: you can use --to=- to output the result in standard output.