Yes, you have to assume that the DNS server that replied is the DNS server that you (or the router) specified.
The [:resolve "microsoft.com"] is a script command, it is not really a troubleshooting tool. I have a number of scripts that relay on [:resolve "microsoft.com"] returning just a single IP-address, any change to it would break scripts for a lot of people.
It would be nice with a real "NSLOOKUP"-style troubleshooting tool though.
In RouterOS version 6.36 and newer, you can also use address lists to get a list of IP-addresses that the DNS name resolve as.
[admin@MikroTestRouter] > /ip firewall address-list add address="microsoft.com" list="list1"
[admin@MikroTestRouter] > /ip firewall address-list print where list="list1"
Flags: X - disabled, D - dynamic
# LIST ADDRESS CREATION-TIME TIMEOUT
0 list1 microsoft.com oct/02/2019 11:38:55
1 D ;;; microsoft.com
list1 126.96.36.199 oct/02/2019 11:38:55
2 D ;;; microsoft.com
list1 188.8.131.52 oct/02/2019 11:38:55
3 D ;;; microsoft.com
list1 184.108.40.206 oct/02/2019 11:38:55
4 D ;;; microsoft.com
list1 220.127.116.11 oct/02/2019 11:38:55
5 D ;;; microsoft.com
list1 18.104.22.168 oct/02/2019 11:38:55
[admin@MikroTestRouter] > /ip firewall address-list remove [find list="list1" !dynamic]
I wish my FTP was FTL.