As well as [mariadb], [server], etc. sections.

Not sure we can do everything. mysql_install_db.exe only creates [mysqld] section. While in theory a lot of sections are possible, in practice I have not seen a my.ini with [mariadb] or with [server]. In worst case, if start with the new version fails, an understandable error message should be extracted from the error log, so people can fix manually And, we should roll back service config change in this case.

list of the variables that were there in either 5.5,10.0,10.1,10.2 and have gone in 10.3 (this excludes loadable plugins, only server and engines compiled in by default)

aria_recover
debug_crc_break
engine_condition_pushdown
have_csv
have_innodb
have_ndbcluster
have_partitioning
innodb_adaptive_flushing_method
innodb_adaptive_hash_index_partitions
innodb_additional_mem_pool_size
innodb_api_bk_commit_interval
innodb_api_disable_rowlock
innodb_api_enable_binlog
innodb_api_enable_mdl
innodb_api_trx_level
innodb_blocking_buffer_pool_restore
innodb_buffer_pool_populate
innodb_buffer_pool_restore_at_startup
innodb_buffer_pool_shm_checksum
innodb_buffer_pool_shm_key
innodb_checkpoint_age_target
innodb_cleaner_eviction_factor
innodb_cleaner_flush_chunk_size
innodb_cleaner_free_list_lwm
innodb_cleaner_lru_chunk_size
innodb_cleaner_lsn_age_factor
innodb_cleaner_max_flush_time
innodb_cleaner_max_lru_time
innodb_corrupt_table_action
innodb_dict_size_limit
innodb_doublewrite_file
innodb_empty_free_list_algorithm
innodb_fake_changes
innodb_fast_checksum
innodb_file_format
innodb_file_format_check
innodb_file_format_max
innodb_flush_neighbor_pages
innodb_foreground_preflush
innodb_ibuf_accel_rate
innodb_ibuf_active_contract
innodb_ibuf_max_size
innodb_import_table_from_xtrabackup
innodb_instrument_semaphores
innodb_kill_idle_transaction
innodb_large_prefix
innodb_lazy_drop_table
innodb_locking_fake_changes
innodb_log_arch_dir
innodb_log_arch_expire_sec
innodb_log_archive
innodb_log_block_size
innodb_log_checksum_algorithm
innodb_max_bitmap_file_size
innodb_max_changed_pages
innodb_merge_sort_block_size
innodb_mirrored_log_groups
innodb_mtflush_threads
innodb_persistent_stats_root_page
innodb_print_lock_wait_timeout_info
innodb_purge_run_now
innodb_purge_stop_now
innodb_read_ahead
innodb_recovery_stats
innodb_recovery_update_relay_log
innodb_safe_truncate
innodb_show_locks_held
innodb_show_verbose_locks
innodb_stats_auto_update
innodb_stats_update_need_lock
innodb_support_xa
innodb_thread_concurrency_timer_based
innodb_track_changed_pages
innodb_track_redo_log_now
innodb_use_fallocate
innodb_use_global_flush_log_at_trx_commit
innodb_use_mtflush
innodb_use_stacktrace
innodb_use_sys_malloc
innodb_use_sys_stats_table
innodb_use_trim
log
log_slow_queries
rpl_recovery_rank
sql_big_tables
sql_low_priority_updates
sql_max_join_size