1.cat file1| awk -F "-" '{print $2}'| sed "s/\.[a-z].*//g">file_1_final.txt
2.cat file2| awk -F "-" '{print $2}'| sed "s/\.[a-z].*//g">file_2_final.txt
3.paste file_1_final.txt file_2_final.txt  | sed '1i file1     file2' >combined_file1_file2
4.awk -F "-"  'NR==FNR{a[$1];next}($1 in a){print $1}' file1 file2>>common_difference_file_1_2
5.awk -F "-"  'NR==FNR{a[$1];next}!($1 in a){print $1}' file1 file2>>common_difference_file_1_2
6.sed -i '1i name' common_difference_file_1_2

Final step
7.paste common_difference_file_1_2 combined_file1_file2

output

name    file1     file2
ap  2.21.3  2.35.3
bp  3.42.4  3.43.4
cp  3.23.2  4.33.2
dp      4.52.4

1. cat file1| awk -F "-" '{print $2}'| sed "s/\.[a-z].*//g">file_1_final.txt
2. cat file2| awk -F "-" '{print $2}'| sed "s/\.[a-z].*//g">file_2_final.txt
3. paste file_1_final.txt file_2_final.txt | sed '1i file1 file2' >combined_file1_file2
4. awk -F "-" 'NR==FNR{a[$1];next}($1 in a){print $1}' file1 file2>>common_difference_file_1_2
5. awk -F "-" 'NR==FNR{a[$1];next}!($1 in a){print $1}' file1 file2>>common_difference_file_1_2
6. sed -i '1i name' common_difference_file_1_2
7. paste common_difference_file_1_2 combined_file1_file2

Output:

name    file1     file2
ap  2.21.3  2.35.3
bp  3.42.4  3.43.4
cp  3.23.2  4.33.2
dp      4.52.4