Why are engineered vectors preferred by biotechnologists for transferring desired genes into another organism?

Cloning vector is a vehicle used to transfer a gene of interest attached to it into a host for its cloning(making copies). They are pieces of DNA which can be extra chromosomal region in bacteria (plasmid), bacteriophages, Yeast artificial chromosome, etc. Vectors are modified  in order to link foreign gene efectively. They contain the cloning sites refer to the recognition sites for restriction enzymes (such as EcoRI, Hind III, PvuI , BamHI, etc). These are the sites where restriction enzymes cut the DNA of vector and insert foreign DNA into it. So, genetically engineered vectors are preferred by biotechnologists. Vectors are also modified for other reasons.
For example: Ti plasmid can be modified into a cloning vector by removing the genes responsible for pathogenicity  and inserting  desired genes such as disease resistance. Then this modified Agrobacterium tumefaciens is allowed to infect plant to introduce desired gene in the plant.