MP4 file ignores subtitle settings in VLC

When playing an MKV movie (h264/aac) with a separate .SRT file, VLC lets me control the looks of subtitles perfectly from the menu.

However, after losslessly converting the MKV/SRT to MP4 with built-in subtitles ("mov_text"), the subtitles are displayed as a small Arial(?) font, and VLC settings have no effect on this.

I thought maybe the MP4 file contained some information on how to display the subtitles that had precedence, but it happens even after I stripped all metadata from the MP4 file.

Is this a bug/feature in VLC? How do I make it adhere to the visual subtitle settings for all sorts of video files.

EDIT: SRT EXAMPLE

1
00:00:00,000 --> 00:00:07,000
Lorem ipsum dolor sit amet,
consectetur adipiscing elit,

2
00:00:09,000 --> 00:00:12,000
sed do eiusmod tempor incididunt
ut labore et dolore magna aliqua.

(etc.)

EDIT: SEE FFMPEG OUTPUT BELOW

ffmpeg -y -i "in.mp4" -i "in.srt" -acodec copy -vcodec copy -scodec mov_text -absf aac_adtstoasc "out.mp4"
ffmpeg version 2.8 Copyright (c) 2000-2015 the FFmpeg developers
built with Apple LLVM version 7.0.0 (clang-700.0.72)
configuration: --prefix=/usr/local/Cellar/ffmpeg/2.8 --enable-shared --enable-pthreads --enable-gpl --enable-version3 --enable-hardcoded-tables --enable-avresample --cc=clang --host-cflags= --host-ldflags= --enable-opencl --enable-libx264 --enable-libmp3lame --enable-libvo-aacenc --enable-libxvid --enable-ffplay --enable-libfdk-aac --enable-nonfree --enable-vda
libavutil 54. 31.100 / 54. 31.100
libavcodec 56. 60.100 / 56. 60.100
libavformat 56. 40.101 / 56. 40.101
libavdevice 56. 4.100 / 56. 4.100
libavfilter 5. 40.101 / 5. 40.101
libavresample 2. 1. 0 / 2. 1. 0
libswscale 3. 1.101 / 3. 1.101
libswresample 1. 2.101 / 1. 2.101
libpostproc 53. 3.100 / 53. 3.100
Input #0, mpegts, from 'in.mp4':
Duration: 00:55:34.20, start: 10.099667, bitrate: 2441 kb/s
Program 1
Stream #0:0[0x100]: Video: h264 (High) ([27][0][0][0] / 0x001B), yuv420p, 1280x720 [SAR 1:1 DAR 16:9], 25 fps, 25 tbr, 90k tbn, 50 tbc
Stream #0:1[0x101]: Audio: aac (LC) ([15][0][0][0] / 0x000F), 48000 Hz, stereo, fltp, 162 kb/s
Stream #0:2[0x102]: Data: timed_id3 (ID3 / 0x20334449)
Input #1, srt, from 'in.srt':
Duration: N/A, bitrate: N/A
Stream #1:0: Subtitle: subrip
Output #0, mp4, to 'out.mp4':
Metadata:
encoder : Lavf56.40.101
Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1280x720 [SAR 1:1 DAR 16:9], q=2-31, 25 fps, 25 tbr, 90k tbn, 90k tbc
Stream #0:1: Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, 162 kb/s
Stream #0:2: Subtitle: mov_text ([8][0][0][0] / 0x0008)
Metadata:
encoder : Lavc56.60.100 mov_text
Stream mapping:
Stream #0:0 -> #0:0 (copy)
Stream #0:1 -> #0:1 (copy)
Stream #1:0 -> #0:2 (subrip (srt) -> mov_text (native))
Press [q] to stop, [?] for help
frame=83215 fps=3113 q=-1.0 Lsize= 958501kB time=00:55:34.08 bitrate=2355.1kbits/s
video:891302kB audio:65022kB subtitle:18kB other streams:0kB global headers:0kB muxing overhead: 0.225788%