Your mom doesn't need a visa to Macau, just show her Taiwan passport to Macau Immigration officer, but she needs an Entry Permit to Hong Kong. If your mom holds the the Entry Permit of Taiwan Residents to the Mainland, she can apply for HK visa annotation on this permit.

thanks for the reply, where can she apply for visa annotation on this permit, if she doesn't have one can she still have her entry permit before our travel which is on March 17?

How come the travel agency did not require her to get an entry permit? According to them it is not needed since the stay is less than 30 days.

Taiwan residents holding a valid "Mainland Travel Permits for Taiwan Residents" (commonly known as "Tai Bao Zheng") may enter Hong Kong as visitor and stay for up to 7 days irrespective of whether they are transitting Hong Kong to/from the Mainland or coming to Hong Kong for visit, provided the normal immigration requirements are met.

Once your mom holds the "Mainland Travel Permits for Taiwan Residents" (commonly known as "Tai Bao Zheng"), she doesn't need to apply for Hong Kong entry permit.