mjhjmtu

I have configured dnsmasq as a local DNS server. Now since my ISP does not resolve some-company.sharepoint.com I want to use Google's servers for the domain sharepoint.com. (See here for the windows solution.)

$ grep "^[^#]" /etc/dnsmasq.conf 
server=/sharepoint.com/8.8.8.8
server=/sharepoint.com/8.8.4.4
listen-address=127.0.0.1

I have configured ǸetworkManager to use dnsmasq

$ cat /etc/NetworkManager/NetworkManager.conf 
# Configuration file for NetworkManager.
# See "man 5 NetworkManager.conf" for details.
[main]
dns=dnsmasq

and restarted.

$ sudo systemctl restart NetworkManager

My resolv.conf now looks like this:

$ cat /etc/resolv.conf
# Generated by NetworkManager
search fritz.box
nameserver 127.0.0.1

Using drill to test:

$ drill some-company.sharepoint.com
;; ->>HEADER<<- opcode: QUERY, rcode: NXDOMAIN, id: 21965
...

While the Google server works...

$ drill some-company.sharepoint.com @8.8.8.8
;; ->>HEADER<<- opcode: QUERY, rcode: NOERROR, id: 48098

The docs describing the server option say this option is general:

Dnsmasq has the ability to direct DNS queries for certain domains to
specific upstream nameservers. This feature was added for use with
VPNs but it is fully general.

I could not recreate the situation you encountered.

I assumed a example domain example.com cannot be resolved by the resolver I use. I configured dnsmasq to send questions having this domain to use 8.8.8.8. And dnsmasq's local instance sent questions of this domain (example.com) to Google DNS Resolver only rather than the default resolver I use.