I wold like support for this idea, It wold be a great improvement

for x in (select application_id from apex_applications
             where WORKSPACE in ('WORKSPACE1', 'WORKSPACE2'))
loop
     sys_export_app(x.application_id, '', '', '', 'BACKUP');
end loop;

create or replace procedure sys_export_app(p_app_id          in number
                      , p_exp_ir_pub_rep  in varchar2
                      , p_exp_ir_priv_rep in varchar2
                      , p_exp_ir_notif    in varchar2
                      , p_ora_dir         in varchar2) as
 l_clob clob;
 l_file_name varchar2(255);
begin
 l_file_name := 'app' || p_app_id || '_export.sql';
 l_clob := wwv_flow_utilities.export_application_to_clob(p_application_id            => p_app_id
                                                       , p_export_ir_public_reports  => p_exp_ir_pub_rep
                                                       , p_export_ir_private_reports => p_exp_ir_priv_rep
                                                       , p_export_ir_notifications   => p_exp_ir_notif);
 DBMS_XSLPROCESSOR.CLOB2FILE(l_clob, p_ora_dir, l_file_name);
end sys_export_app;

and from system zip!

declare
   l_files       apex_t_export_files;
   l_all_files   apex_t_export_files := apex_t_export_files();
   l_zip         blob;
   l_export      apex_data_export.t_export;
   l_original_id boolean := (:P4_ORIGIONAL_ID = 'Y');
   l_app_ids     apex_t_varchar2;
begin
   l_app_ids := apex_string.split(:P4_SEL_APP_ID, ',');

   for i in 1 .. l_app_ids.count loop
       l_files := apex_export.get_application(
                      p_application_id     => l_app_ids(i),
                      p_with_original_ids  => l_original_id,
                      p_with_date          => true,
                      p_with_comments      => true
                  );
       l_all_files := l_all_files multiset union all l_files;
   end loop;

   if l_app_ids.count > 1 or :P4_ZIPFILE = 'Y' then
       l_zip := apex_export.zip(p_source_files => l_all_files);
       l_export.content_blob := l_zip;
       l_export.mime_type    := 'application/zip';
       l_export.file_name    := case 
                                    when l_app_ids.count > 1 then 'apps_export.zip'
                                    else 'f' || l_app_ids(1) || '.zip'
                                end;
       l_export.format       := 'zip';
       l_export.as_clob      := false;
   else
       l_export.content_clob := l_all_files(1).contents;
       l_export.mime_type    := 'text/plain';
       l_export.file_name    := 'f' || l_app_ids(1) || '.sql';
       l_export.format       := 'sql';
       l_export.as_clob      := true;
   end if;

   apex_data_export.download(p_export => l_export);
end;

P4_ORIGIONAL_ID  - Incase you want the option like original id then use this page item to set value dynamically

for a single file you want as zipfile or non zipfile you've option to pass dynamcially with the help of P4_ZIPFILE  item

Demo_Application_Link