The Gun Control Act definition in 27CFR§478.11
Antique firearm. (a) Any firearm (including any firearm with a
matchlock, flintlock, percussion cap, or similar type of ignition
system) manufactured in or before 1898; and (b) any replica of any
firearm described in paragraph (a) of this definition if such replica
(1) is not designed or redesigned for using rimfire or conventional
centerfire fixed ammunition, or (2) uses rimfire or conventional
centerfire fixed ammunition which is no longer manufactured in the
United States and which is not readily available in the ordinary
channels of commercial trade.
The bolded part stands alone, and is not modified by any following part of the paragraph. Any firearm manufactured in or before 1898.
Your confusion comes from '(1)' and '(2)' which modify 'any replica of any
firearm described in paragraph (a)'. Notice the underlined part, which clearly shows the rest of the paragraph is defining 'if such replica'.
Hence it is replicas of such firearms that must not be center fire, or rimfire, or use ammunition not readily available through regular trade, to meet the definition of 'antique'.
An actual firearm made before 1898 is not a replica.
Also, the way parenthesis work, what is in them could be omitted without destroying the meaning of the statement. "(including any firearm with a
matchlock, flintlock, percussion cap, or similar type of ignition
system)". So it would only be an addition. It is 'including' all of those ignition types listed in addition, but not excluding 'Any firearm manufactured in or before 1898' which is not one of those types.
Now this section though is different:
The National Firearms Act definition in 27CFR§479.11
Antique firearm. Any firearm not designed or redesigned for using rim fire or conventional center fire ignition with fixed ammunition and
manufactured in or before 1898 (including any matchlock, flintlock,
percussion cap, or similar type of ignition system or replica thereof,
whether actually manufactured before or after the year 1898) and also
any firearm using fixed ammunition manufactured in or before 1898, for
which ammunition is no longer manufactured in the United States and is
not readily available in the ordinary channels of commercial trade.
In this section of law the requirement is both 'Any firearm not designed or redesigned for using rim fire or conventional center fire ignition with fixed ammunition' '
AND' 'manufactured in or before 1898'.
The clear meaning of 'and' absent other punctuation or proceeding to deal with another topic as is used in this section makes both requirements necessary to meet the definition of 'antique'.
It then goes on to say all firearms 'matchlock, flintlock, percussion cap, or similar type of ignition system or replica thereof, whether actually manufactured before or after the year 1898' are also included.
So clearly the definitions under 27CFR§479.11 and 27CFR§478.11 are different, even though they may appear very similar out of legal context.
A firearm can become an antique under one without qualifying as an antique under the other. The primary difference is 27CFR§478.11 makes all firearms made before 1898 antiques, period.
While 27CFR§479.11 requires those made before or during 1898 either not be center fire or rim fire, or have ammunition not available through regular trade (which clearly in the day of the internet is a big ATF discretion area as someone somewhere will make anything.)