Всё забывал написать, как всё пришло в норму.
На другой домен поставил свежий опенкарт, включил там поддержку SEO URL, переименовал .htaccess, отредактировал пару категорий (сделал им SEO URL) и на удивление всё заработало. Ради интереса копирнул .htaccess в корень http://feeder-sib.ru и на удивление всё заработало. Странность в том, что пока не озадачился включением SEO URL, я .htaccess вообще не трогал.
Привожу тело .htaccess:
# 1.To use URL Alias you need to be running apache with mod_rewrite enabled.
# 2. In your opencart directory rename htaccess.txt to .htaccess.
# For any support issues please visit: http://www.opencart.com
Options +FollowSymlinks
# Prevent Directoy listing
Options -Indexes
# Prevent Direct Access to files
<FilesMatch "\.(tpl|ini|log)">
Order deny,allow
Deny from all
</FilesMatch>
# SEO URL Settings
RewriteEngine On
# If your opencart installation does not run on the main web folder make sure you folder it does run in ie. / becomes /shop/
RewriteBase /
RewriteRule ^sitemap.xml$ index.php?route=feed/google_sitemap [L]
RewriteRule ^googlebase.xml$ index.php?route=feed/google_base [L]
RewriteRule ^download/(.*) /index.php?route=error/not_found [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !.*\.(ico|gif|jpg|jpeg|png|js|css)
RewriteRule ^([^?]*) index.php?_route_=$1 [L,QSA]
### Additional Settings that may need to be enabled for some servers
### Uncomment the commands by removing the # sign in front of it.
### If you get an "Internal Server Error 500" after enabling any of the following settings, restore the # as this means your host doesn't allow that.
# 1. If your cart only allows you to add one item at a time, it is possible register_globals is on. This may work to disable it:
# php_flag register_globals off
# 2. If your cart has magic quotes enabled, This may work to disable it:
# php_flag magic_quotes_gpc Off
# 3. Set max upload file size. Most hosts will limit this and not allow it to be overridden but you can try
# php_value upload_max_filesize 999M
# 4. set max post size. uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value post_max_size 999M
# 5. set max time script can take. uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value max_execution_time 200
# 6. set max time for input to be recieved. Uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value max_input_time 200
# 7. disable open_basedir limitations
# php_admin_value open_basedir none
Вот ссылки, в подтверждение того, что работает:
feeder-sib.ru/kormushki_plastikovie_dlya_ribalki_kupit_ribolovnii_internet_magazin_novosibirsk/fidernie_kormushki_ahs/ahs_bolshie/ahs_otkritaya_oval_bez_krilev
feeder-sib.ru/udochki_dlya_ribalki_kupit_ribolovnii_internet_magazin_novosibirsk/Garbolino_udochki/fidernye-i-pikernye-udilishha-garbolino-g-sistem/Pikernoe-udiliwe-g-system-picker-3m-10-35-gr
feeder-sib.ru/prikormka_dobavka_aromatizator_dlya_ribalki_kupit_ribolovnii_internet_magazin_novosibirsk/traper_dlya_ribnoi_lovli_nsk/zhidkie_dobavki/aromatizatory_aromat_250_ml/Aromat_Bream_Secret