Database Errors During WordPress Update 6.3

I recently upgraded my WordPress installation on one of my staging sites to version 6.3. Post-upgrade, when I press the update database button as requested, I encountered multiple database errors related to primary keys and duplicate key names across various tables such as wp_usermeta, wp_termmeta, wp_term_taxonomy, etc.

Is it still safe to use Index WP MySQL For Speed and keep the indexes during upgrades? Here the full error message:

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_usermeta ADD PRIMARY KEY (umeta_id)

WordPress database error: [Duplicate key name 'user_id']
ALTER TABLE wp_usermeta ADD KEY user_id (user_id)

WordPress database error: [Duplicate key name 'meta_key']
ALTER TABLE wp_usermeta ADD KEY meta_key (meta_key(191))

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_termmeta ADD PRIMARY KEY (meta_id)

WordPress database error: [Duplicate key name 'term_id']
ALTER TABLE wp_termmeta ADD KEY term_id (term_id)

WordPress database error: [Duplicate key name 'meta_key']
ALTER TABLE wp_termmeta ADD KEY meta_key (meta_key(191))

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_term_taxonomy ADD PRIMARY KEY (term_taxonomy_id)

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_commentmeta ADD PRIMARY KEY (meta_id)

WordPress database error: [Duplicate key name 'comment_id']
ALTER TABLE wp_commentmeta ADD KEY comment_id (comment_id)

WordPress database error: [Duplicate key name 'meta_key']
ALTER TABLE wp_commentmeta ADD KEY meta_key (meta_key(191))

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_comments ADD PRIMARY KEY (comment_ID)

WordPress database error: [Duplicate key name 'comment_approved_date_gmt']
ALTER TABLE wp_comments ADD KEY comment_approved_date_gmt (comment_approved,comment_date_gmt)

WordPress database error: [Duplicate key name 'comment_date_gmt']
ALTER TABLE wp_comments ADD KEY comment_date_gmt (comment_date_gmt)

WordPress database error: [Duplicate key name 'comment_parent']
ALTER TABLE wp_comments ADD KEY comment_parent (comment_parent)

WordPress database error: [Duplicate key name 'comment_author_email']
ALTER TABLE wp_comments ADD KEY comment_author_email (comment_author_email(10))

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_options ADD PRIMARY KEY (option_id)

WordPress database error: [Multiple primary key defined]
ALTER TABLE wp_postmeta ADD PRIMARY KEY (meta_id)

WordPress database error: [Duplicate key name 'post_id']
ALTER TABLE wp_postmeta ADD KEY post_id (post_id)

WordPress database error: [Duplicate key name 'meta_key']
ALTER TABLE wp_postmeta ADD KEY meta_key (meta_key(191))

WordPress database error: [Duplicate key name 'type_status_date']
ALTER TABLE wp_posts ADD KEY type_status_date (post_type,post_status,post_date,ID)

WordPress database error: [Duplicate key name 'post_parent']
ALTER TABLE wp_posts ADD KEY post_parent (post_parent)

WordPress database error: [Duplicate key name 'post_author']
ALTER TABLE wp_posts ADD KEY post_author (post_author)