merging requires a lot more compute than an overwrite.
It has to check which files to replace.
If your data is very skewed, f.e. 60 or more percent of the data resides in a single file, that will be the bottleneck.
For merges to go fast one can use optimizations (like liquid clustering) or partition the table and do partition pruning while merging (basically an added where clause on the partition column).